Microorganisms having increased lipid productivity

ABSTRACT

The present invention provides mutant microorganism that have higher lipid productivity than the wild type microorganisms from which they are derived while biomass at levels that are within approximately 50% of wild type biomass productivities under nitrogen replete conditions. Particular mutants produce at least twice as much FAME lipid as wild type while producing at least 75% of the biomass produced by wild type cells under nitrogen replete conditions. Also provided are methods of producing lipid using the mutant strains.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation application of U.S. application Ser.No. 16/790,631 filed Feb. 13, 2020 which is a continuation applicationof U.S. application Ser. No. 16/267,940 filed Feb. 5, 2019, now issuedas U.S. Pat. No. 10,563,232; which is a divisional application of U.S.application Ser. No. 15/210,845 filed Jul. 14, 2016, now issued as U.S.Pat. No. 10,227,619; which claims the benefit under 35 USC § 119(e) toU.S. Application Ser. No. 62/318,161 filed Apr. 4, 2016 and to U.S.Application Ser. No. 62/192,510 filed Jul. 14, 2015, both now expired.The disclosure of each of the prior applications is considered part ofand is incorporated by reference in the disclosure of this application.

INCORPORATION BY REFERENCE OF SEQUENCE LISTING

The material in the accompanying sequence listing is hereby incorporatedby reference into the application. The accompanying sequence listingtext file, named SGI1920-5_Sequence_Listing.txt, was created on Oct. 14,2020 and is 229 KB in size. The file can be accessed using MicrosoftWord on a computer that uses Window OS.

BACKGROUND OF THE INVENTION

The invention relates to mutant microorganisms, such as algae andheterokonts, having increased lipid productivity and their use inproducing lipids.

Many microorganisms such as algae, labyrinthulomycetes (“chytrids”), andoleaginous yeast induce lipid biosynthesis in response to nutrientstress, for example nitrogen starvation. Under conditions of nitrogendepletion, such microorganisms redirect compound biosynthesis fromprotein to storage lipids, typically triacylglyceride lipids (“TAG”).Because nitrogen depletion simultaneously decreases cell growth, optimallipid biosynthesis is limited to a relatively short window before thecells become too metabolically impaired to maintain high levels ofproduction.

Microalgal-derived biodiesel has long been considered a viablealternative to conventional petroleum-based fuels. However, despitedecades of biological research, depriving strains of essentialmacronutrients such as nitrogen, phosphorous, or silicon, to obtain highlipid yields—conditions under which growth of the host microorganism iscompromised—remains the modus operandi. Little progress has been made inengineering algal strains to accumulate lipid while maintaining growthas there is only nascent understanding of the regulation of metabolismunderlying lipid accumulation (Courchesne et al. (2009) J. Biotechnol.141:31-41; Goncalves et al. (2016) Plant Biotechnol. J. doi:1111/12523)

Various attempts to improve lipid productivity by increasing lipidbiosynthesis during nutrient replete growth have focused on manipulatinggenes encoding enzymes for nitrogen assimilation or lipid metabolism aswell as genes encoding polypeptides involved in lipid storage. Forexample, US2014/0162330 discloses a Phaeodactylum tricornutum strain inwhich the nitrate reductase (NR) gene has been attenuated by RNAi-basedknockdown; Trentacoste et al. ((2013) Proc. Natl. Acad. Sci. USA 110:19748-19753) disclose diatoms transformed with an RNAi constructtargeting the Thaps3_264297 gene predicted to be involved in lipidcatabolism; and WO2011127118 discloses transformation of Chlamydomonaswith genes encoding oleosins (lipid storage protein) as well as withgenes encoding diacylglycerol transferase (DGAT) genes. Although in eachcase increased lipid production was asserted based on microscopy orstaining with lipophilic dyes, no quantitation of lipid by themanipulated cells was provided, nor was the relationship between biomassand lipid productivities over time determined.

WO 2011/097261 and US 2012/0322157 report that a gene denoted “SN03”encoding an arrestin protein has a role in increasing lipid productionunder nutrient replete conditions when overexpressed in Chlamydomonas.However, overexpression of the SN03 gene was observed to result in theappearance of unidentified polar lipids, which were not quantified, anddid not result in an increase in triglycerides (TAG). Anotherpolypeptide identified as potentially regulating stress-induced lipidbiosynthesis has been described by Boyle et al. ((2012) J. Biol. Chem.287:15811-15825). Knockout of the NRR1 gene in Chlamydomonas encoding a“SQUAMOUSA” domain polypeptide resulted in a reduction of lipidbiosynthesis with respect to wild type cells under nitrogen depletion;however, no mutants were obtained demonstrating increased lipidproduction. US 2010/0255550 recommends the overexpression of putativetranscription factors (“TF1, TF2, TF3, TF4, and TF5”) in algal cells toincrease lipid production, but no mutants having enhanced lipidproduction are disclosed.

Daboussi et al. 2014 (Nature Comm. 5:3881) report that disruption of theUGPase gene in Phaeodactylum triconornutum, which is believed to provideprecursors to laminarin (storage carbohydrate) synthesis, results inincreased lipid accumulation. However, no biochemical data was shown toindicate that laminarin content was affected and lipid and biomassproductivities were not reported. Similarly, several groups havereported increases in lipid accumulation in Chlamydomonas starchlessmutants (Wang et al. 2009 Eukaryotic Cell 8:1856-1868; Li et al. 2010Metab Eng. 12:387-391) but successive reports that actually measuredlipid productivity concluded that these strains were impaired in growthwhen grown in phototrophic conditions (Siaut et al. 2011 BMC Biotechnol.11:7; Davey et al. 2014 Eukaryot Cell 13:392-400). These reportsconcluded that the highest lipid productivities (measured as TAG perliter per day) were actually achieved by the wild-type parental strain.

SUMMARY OF THE INVENTION

Algal mutants having elevated levels of constitutive lipid productionare provided herein. As demonstrated in the examples, analysis of earlytranscriptional profiles of Nannochloropsis gaditana to N-deprivationrevealed a novel negative regulator of lipid biosynthesis ZnCys-2845, atranscription factor of the fungal Zn(II)2Cys6 gene family. UsingCas9-mediated mutagenesis and RNAi technology, attenuated ZnCys strainswere produced that were capable of partitioning approximately 45% oftheir total carbon content to lipids and of sustaining growth in acontinuous growth system, resulting in a doubling of lipid productivity.

A first aspect of the invention is a mutant microorganism that producesat least 25% more lipid than is produced by a control microorganismwhile producing not less than 45% of the biomass produced by the controlmicroorganism cultured under the same conditions, in which the cultureconditions support production of biomass by the control microorganism.For example, a mutant microorganism as provided herein can produce atleast 30%, at least 40%, at least 50%, at least 60%, at least 70%, atleast 80%, at least 90%, or at least 100% more lipid than is produced bya control microorganism cultured under the same conditions as the mutantmicroorganism, which can be batch, semi-continuous, or continuousculture conditions, and in various embodiments are culture conditions inwhich the control microorganism accumulates biomass. The controlmicroorganism can be, in some examples, a wild type microorganism, i.e.,a wild type microorganism from which the mutant microorganism isdirectly or indirectly derived. The mutant microorganism can produce, invarious embodiments, at least about 50% of the biomass and at leastabout 50%, at least 55%, at least 60%, at least 70%, at least 75%, atleast 80%, at least 85%, at least 90%, at least 95%, at least 100%, atleast 110%, or at least 120% more lipid than is produced by a controlmicroorganism cultured under the same conditions, where the controlmicroorganism produces biomass, for example, produces biomass over thecourse of the culture or on a daily basis, under the culture conditionsin which the mutant produces more lipid. In various examples a mutantmicroorganism as provided herein produces at least 50% of the biomassand at least 130%, at least 150%, at least 140%, at least 155%, at least160%, at least 170%, at least 175%, at least 180%, at least 185%, atleast 190%, at least 195%, at least 200%, at least 210%, or at least215% of the amount of lipid produced by a wild type microorganismcultured under the same conditions, under which the wild typemicroorganism accumulates biomass. For example, the culture conditionscan be nitrogen-replete with respect to the control or wild typemicroorganism.

A mutant microorganism as provided herein can produce at least 25% moreFAME lipids than a control or wild type microorganism while producing atleast 45% or at least about 50% as much biomass as the control or wildtype microorganism over a culture period of at least three days, atleast five days, at least seven days, at least eight days, at least tendays, at least twelve days, at least fifteen days, at least twenty days,at least thirty days, or at least sixty days. For example, the averagedaily FAME productivity can be at least 50% greater than that of acontrol or wild type microorganism while the average daily biomass(e.g., TOC) productivity can be at least 45% or at least about 50% thatof the control or wild type microorganism over a culture period of atleast three days, at least five days, at least seven days, at least tendays, at least twelve days, at least fifteen days, at least twenty days,at least thirty days, or at least sixty days. In particular examples, amutant microorganism as provided herein can produce at least 50% moreFAME lipids than a control or wild type microorganism while producing atleast 60% as much biomass as the control microorganism over a cultureperiod of at least seven days, at least eight days, or at least ten dayswhere the daily amount of FAME produced by the mutant is not lower thanthe daily amount of FAME produced by the control or wild typemicroorganism on any day during the at least seven, at least eight, orat least ten day culture period. In further examples, the average dailyFAME productivity of a mutant microorganism as provided herein can be atleast 50% higher than the average daily FAME productivity of a controlor wild type microorganism the average daily biomass productivity can beat least 50% of the average daily biomass productivity of the controlmicroorganism over a culture period of at least seven days, at leasteight days, or at least ten days where the daily amount of FAME producedby the mutant is not lower than the daily amount of FAME produced by thecontrol or wild type microorganism on any day during the at least seven,at least eight, or at least ten day culture period.

For example, a mutant microorganism as provided herein can produce moreFAME-derivatizable lipids (“FAME lipids” or “FAME”) than a controlmicroorganism while producing not less than 45% of the biomass producedby the control microorganism, when the mutant microorganism and controlmicroorganism are cultured under the same culture conditions under whichthe control microorganism produces biomass. A mutant microorganism asprovided herein can have greater average daily FAME productivity than acontrol microorganism while exhibiting at least 45% of the average dailybiomass productivity of the control microorganism, when the mutantmicroorganism and control microorganism are cultured under the sameculture conditions under which the control microorganism producesbiomass. In various examples, a mutant microorganism as provided hereinproduces at least 50% more FAME lipids while producing not less thanabout 50%, not less than about 60%, or not less than about 70% of thebiomass produced by the control microorganism, when the mutantmicroorganism and control microorganism are cultured under the sameculture conditions under which the culture of the control microorganismproduces biomass, which can be nitrogen-replete culture conditions withrespect to the control microorganism. The control microorganism invarious embodiments can be a wild type microorganism, e.g., a wild typemicroorganism from which the mutant microorganism is directly orindirectly derived.

In some examples, the culture conditions under which the mutant producesmore lipid than a control or wild type microorganism can be cultureconditions in which the concentration of ammonium in the culture mediumis less than about 2.5 mM, for example, less than about 2 mM, less thanabout 1.5 mM, less than about 1 mM, or less than or equal to about 0.5mM. In some examples the culture medium can include no added ammonium orsubstantially no ammonium. In some examples, the culture medium caninclude no added source of reduced nitrogen for the microorganism, e.g.,no added ammonium, urea, or amino acids that can be metabolized by themicroorganism. The culture medium can in some examples include anitrogen source such as, but not limited to, nitrate. Alternatively orin addition, the culture medium can include urea. In some examples, theculture medium is nutrient replete with respect to a wild typemicroorganism of the species from which the mutant microorganism isderived.

In various embodiments, the mutant microorganism can be a photosyntheticmicroorganism and the mutant microorganism can produce at least 25% moreFAME lipids than a control microorganism while producing at least 45%,at least 50%, at least 60%, at least 70%, at least 80%, at least 90% orat least 95% the amount of biomass as a control or wild typemicroorganism under photoautotrophic culture conditions. For example amutant microorganism as provided herein can be an alga, such as aeukaryotic microalga, and can produce at least 25% more FAME lipids thana control or wild type microorganism while producing at least 45%, atleast 50%, at least 60%, at least 70%, at least 80%, at least 90% or atleast 95% the amount of biomass as a control microorganism when both thecontrol microorganism are cultured using inorganic carbon assubstantially the sole source of carbon in the cultures. The controlmicroorganism can be, for example, a wild type microorganism.

Culture conditions in which a mutant microorganism as provided hereincan produce more FAME lipids than a control or wild type microorganismwhile producing at least 45%, at least 50%, at least 60%, at least 70%,at least 80%, at least 90% or at least 95% the amount of biomass as acontrol or wild type microorganism include any of batch, continuous, orsemi-continuous culture conditions in which the control or wild typemicroorganism produces biomass. In various embodiments, a mutantmicroorganism as provided herein can produce at least 50% more FAMElipids than a control or wild type microorganism while producing atleast 45%, at least about 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, orat least 95% as much biomass as the control or wild type microorganismover a culture period of at least three days, at least four days, atleast five days, at least seven days, at least eight days, at least tendays, or at least twelve days. In some embodiments the average dailyFAME productivity of a mutant microorganism is at least 50% more thanthat of a control or wild type microorganism while the average dailybiomass productivity (e.g., TOC productivity) is at least 45%, at leastabout 50%, at least 55%, at least 60%, at least 65%, at least 70%, atleast 75%, at least 80%, at least 85%, at least 90%, or at least 95% asgreat as that of the control or wild type microorganism over the cultureperiod, for example, over a culture period of at least three days, atleast four days, at least five days, at least seven days, at least tendays, or at least twelve days.

In some examples, a mutant microorganism as provided herein can produceat least 50% more FAME lipids while producing at least about 75% of theamount of biomass produced by a wild type or control microorganismduring a culture period of at least three, at least four, at least five,at least six, at least seven, at least eight, at least nine, at leastten, at least eleven, at least twelve, or at least thirteen days, forexample, over a culture period of at least five, at least ten, at leastfifteen, at least twenty, or at least thirty days where the mutant andcontrol microorganism are cultured under the same conditions, underwhich both the mutant and control microorganisms produce biomass. Forexample, a mutant microorganism can demonstrate at least 60%, at least70%, at least 80%, at least 90%, at least 100%, or at least 110%, or atleast 120% higher FAME productivity and exhibit no more than a 35%, 30%,25%, 20%, 15%, 10%, 5%, 2%, or 1% decline in biomass (e.g., TOC)productivity with respect to a wild type or control microorganismcultured for at least five, at least six, at least seven, or at leasteight days under conditions in which both the control and mutantmicroorganism cultures produce biomass. For example, the average dailyFAME productivity of a mutant as provided herein can be at least 60%, atleast 70%, at least 80%, at least 90%, at least 100%, or at least 110%more than that of a wild type or control microorganism and the averagedaily biomass (e.g., TOC) productivity can be at least about 50%, atleast about 60%, at least about 70%, or at least about 80% of theaverage daily biomass productivity of the control microorganism underconditions in which both the control and mutant microorganism culturesare producing biomass. In various embodiments, the average daily FAMEproductivity of a mutant as provided herein can be at least 60%, atleast 70%, at least 80%, at least 90%, at least 100%, or at least 110%more than that of a wild type or control microorganism and the averagedaily biomass (e.g., TOC) productivity can be at least about 50%, atleast about 60%, at least about 70%, or at least about 80% of theaverage daily biomass productivity of the control microorganism underconditions in which both the control and mutant microorganism culturesare producing biomass on a daily basis. In some examples, a mutantmicroorganism can produce at least 100% more or at least 120% more FAMElipids than a wild type or control microorganism while producing atleast about 75% or at least about 80% of the biomass produced by acontrol type microorganism cultured under identical conditions which arenitrogen replete with respect to the control microorganism. In otherexamples a mutant microorganism can produce at least 75%, at least 80%,at least 85% more FAME lipids than a wild type or control microorganismwhile producing approximately as much biomass as is produced by a wildtype microorganism cultured under identical conditions under which thewild type or control microorganism produces biomass, e.g., within 10% orwithin 5% of the amount of biomass produced by the controlmicroorganism. In various examples, the average daily FAME productivityfor at least three, at least four, at least five, at least six, at leastseven, at least eight, at least nine, at least ten, at least eleven, atleast twelve, or at least thirteen days of culturing, for example, atleast five, at least ten, at least fifteen, at least twenty, or at leastthirty days of culturing can be at least 80% greater than the averagedaily FAME productivity of a wild type or control microorganism and theaverage daily biomass productivity can be substantially the same as thatof a control or wild type microorganism cultured under identicalconditions under which the wild type or control microorganism producesbiomass, e.g., within 10%, within 5%, or within 2% of the biomassproductivity of the control microorganism. The conditions in which amutant microorganism produces at least 80% more FAME lipids than a wildtype or control microorganism while producing at least as much biomassas produced by a wild type microorganism can be nutrient replete withrespect to the wild type or control microorganism, and can be nitrogenreplete with respect to the wild type or control microorganism. Invarious embodiments the mutant microorganism can be a photosyntheticmicroorganism, e.g., an alga, and the culture conditions under which themutant alga has greater FAME productivity while producing at least 50%of the TOC as a control microorganism are photoautotrophic conditions.

A mutant microorganism as provided herein can have a FAME lipids (FAME)to total organic carbon (TOC) ratio at least 30% higher than theFAME/TOC ratio of the control microorganism under culture conditions inwhich the mutant microorganism produces at least 45% more FAME lipidsand at least 50% as much biomass as the control microorganism. TheFAME/TOC ratio of a mutant microorganism as provided herein can be, forexample, at least 30% higher, at least 40% higher, at least 50% higher,at least 60% higher, at least 70% higher, at least 80% higher, at least90% higher, at least 100% higher, at least 110% higher, at least 120%higher, at least 130% higher, at least 140% higher, at least 150%higher, or at least 200% higher than the FAME/TOC ratio of a control orwild type microorganism cultured under identical conditions under whichthe control or wild type organism produces biomass, which may benitrogen replete with respect to the wild type microorganism. In variousembodiments, the FAME/TOC ratio of the mutant is at least 0.3, at least0.4, at least 0.5, at least 0.6, at least 0.7, or at least 0.8 while themutant microorganism culture is accumulating TOC. For example, a mutantmicroorganism as provided herein can have at least 25% higher lipidproductivity than a control microorganism while exhibiting not less than45% or not less than about 50% of the average daily biomass productivityof the control microorganism, and can further have FAME lipids(FAME)/total organic carbon (TOC) ratios at least 30%, at least 50%, atleast 70%, or at least 90% higher than the FAME/TOC ratio of a wild typemicroorganism, for at least three, at least four, at least five, atleast six, at least seven, at least eight, at least nine, at least ten,at least eleven, at least twelve, at least thirteen, at least fifteen,at least twenty, at least twenty-five, at least thirty, or at leastsixty days of culturing, when the mutant microorganism and controlmicroorganism are cultured under the same culture conditions in whichboth the mutant microorganism and control microorganism accumulatebiomass, e.g., accumulate biomass on a daily basis. In variousembodiments, the FAME/TOC ratio of the mutant is at least 0.3, at least0.4, at least 0.5, at least 0.6, at least 0.7, at least 0.8, or betweenabout 0.35 and 0.85, or between about 0.4 and about 0.8 while the mutantmicroorganism produces at least 50% of the TOC produced by the controlmicroorganism over a period of at least three, at least four, at leastfive, at least six, at least seven, at least eight, at least nine, atleast ten, at least eleven, at least twelve, at least thirteen, at leastfifteen, at least twenty, at least twenty-five, at least thirty, or atleast sixty days of culturing, where the mutant and controlmicroorganism are cultured under the same conditions and the mutantproduces more lipid than the control microorganism, and both the mutantmicroorganism and the control microorganism produce biomass.

Thus, a further aspect of the invention is a mutant microorganism thatexhibits a higher FAME/TOC ratio than is exhibited by a controlmicroorganism when both the mutant microorganism and controlmicroorganism are cultured under substantially identical conditionsunder which both the mutant microorganism and the control microorganismculture are accumulating TOC. In various examples, a mutantmicroorganism has a higher FAME/TOC ratio than is exhibited by a controlmicroorganism when the mutant microorganism and control microorganismare cultured under identical conditions under which both the controlmicroorganism and the mutant microorganism produce biomass and themutant microorganism culture produces at least about 50%, at least 60%,at least 70%, at least 80%, at least 90%, at least 95%, or about orsubstantially the same amount of TOC as the wild type microorganismculture. The FAME/TOC ratio of a mutant microorganism as provided hereincan be, for example, at least 30% higher, at least 40% higher, at least50% higher, at least 60% higher, at least 70% higher, at least 80%higher, at least 90% higher, at least 100% higher, at least 110% higher,at least 120% higher, at least 130% higher, at least 140% higher, or atleast 150% higher than the FAME/TOC ratio of a control or wild typemicroorganism during a culture period in which the mutant microorganismproduces at least about 50%, at least 60%, at least 70%, at least 80%,at least 90%, at least 95%, or substantially the same amount of TOC asthe wild type microorganism culture. For example, the average dailybiomass productivity of a mutant microorganism can be at least about50%, at least 60%, at least 70%, at least 80%, at least 90%, at least95%, that of a control or wild type microorganism culture, while havinga FAME/TOC ratio at least 30% higher, at least 40% higher, at least 50%higher, at least 60% higher, at least 70% higher, at least 80% higher,at least 90% higher, at least 100% higher, at least 110% higher, atleast 120% higher, at least 130% higher, at least 140% higher, or atleast 150% higher than the FAME/TOC ratio of a control or wild typemicroorganism averaged over the same time period.

A mutant microorganism as provided herein, e.g., a mutant microorganismsuch as any described herein that produces at least about 50% of thebiomass and at least about 50%, at least 55%, at least 60%, at least70%, at least 75%, at least 80%, at least 85%, at least 90%, at least95%, at least 100%, at least 110%, or at least 120% more lipid than isproduced by a control microorganism cultured under the same conditions,where the conditions support biomass accumulation by the controlmicroorganism, can have a higher carbon to nitrogen (C:N) ratio than acontrol microorganism. For example, the C:N ratio can be from about 1.5to about 2.5 times the C:N ratio of a control microorganism when themutant microorganism and the control microorganism are cultured underconditions in which both the mutant and the control microorganismsaccumulate biomass, and the mutant produces at least 50%, at least 60%,at least 70%, at least 80%, at least 90% or at least 100% more lipidthat the control microorganism and at least 50%, at least 60%, at least70%, at least 80%, or at least 85% of the TOC of the controlmicroorganism. A mutant microorganism as provided herein, e.g., a mutantmicroorganism such as any described herein that produces at least about50% of the biomass and at least about 50%, at least 55%, at least 60%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 95%, at least 100%, at least 110%, or at least 120% more lipidthan is produced by a control microorganism cultured under the sameconditions, where the conditions support daily biomass accumulation bythe control microorganism, can have a higher carbon to nitrogen (C:N)ratio than a control microorganism. For example, the C:N ratio can befrom about 1.5 to about 2.5 times the C:N ratio of a controlmicroorganism when the mutant microorganism and the controlmicroorganism are cultured under conditions in which both the mutant andthe control microorganisms accumulate biomass on a daily basis, and themutant produces at least 50%, at least 60%, at least 70%, at least 80%,at least 90% or at least 100% more lipid that the control microorganismand at least 50%, at least 60%, at least 70%, at least 80%, or at least85% of the TOC of the control microorganism. In some embodiments the C:Nratio of a mutant as provided herein is between about 7 and betweenabout 20, or between about 8 and about 17, or between about 10 and about15, during the culture period in which mutant produces at least 50% morelipid that a control microorganism while producing at least 50% as muchbiomass as the control microorganism. A control microorganism in any ofthe embodiments or examples herein can be a wild type microorganism.

Alternatively or in addition, mutant microorganism as provided herein,e.g., a mutant microorganism such as any described herein that producesat least about 50% of the biomass and at least about 50%, at least 55%,at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 95%, at least 100%, at least 110%, or at least 120%more lipid than is produced by a control microorganism cultured underthe same conditions, where the conditions support biomass accumulationby the control microorganism (e.g., where the conditions support dailybiomass accumulation by the control microorganism), can have reducedprotein content when compared with a control microorganism. For example,a mutant microorganism as provided herein can have a decrease in proteincontent of at least 10%, at least 20%, at least 30%, at least 40%, atleast 45%, or at least 50% with respect to a control microorganism. Themutant microorganism can partition at least 35%, at least 40%, or atleast about 45% of its total carbon to lipid while producing at least50% more lipid than a control microorganism under the same cultureconditions in which the mutant microorganisms produces at least 65%, atleast 70%, at least 75%, at least 80% as much biomass as the controlmicroorganism.

Further, a mutant microorganism such as any provided herein can in someembodiments have attenuated expression of a gene encoding a proteinwhose expression affects the expression of other genes, e.g., at leastten, at least twenty, at least thirty, at least forty, at least fifty,at least sixty, at least seventy, at least eighty, at least ninety, orat least 100 additional genes. For example, a mutant as provided hereincan have at least ten genes that are upregulated with respect to a wildtype microorganism and at least ten genes that are downregulated withrespect to a wild type microorganism under conditions in which themutant phenotype (as disclosed herein) is displayed. A mutant asprovided herein can have at least twenty, at least thirty, at leastforty, at least fifty, at least sixty, at least seventy, at leasteighty, at least ninety, or at least 100 genes that are upregulated withrespect to a wild type microorganism and at least twenty, at leastthirty, at least forty, at least fifty, at least sixty, at leastseventy, at least eighty, at least ninety, or at least 100 genes thatare downregulated with respect to a wild type microorganism underconditions in which the mutant phenotype (e.g., greater lipid productionwith respect to the wild type microorganism) is expressed. In someembodiments, genes encoding polypeptides involved in protein synthesiscan be upregulated in a mutant as provided herein, for example, genesencoding ribosomal polypeptides or other polypeptides that function inprotein translation, including, without limitation, those belonging togene ontology (GO) groups such as “translation”, “ribosome”, and/or“regulation of translation initiation”. Alternatively to or incombination with the upregulation of genes encoding polypeptidesrelating to protein synthesis, one or more genes encoding polypeptidesinvolved in nitrogen assimilation such as one or more of a nitritereductase, glutamine synthetase, ammonium transporter and/or an enzymeinvolved in molybdenum cofactor biosynthesis can be downregulated in amutant as provided herein. Alternatively or in combination with any ofthe above, a mutant as provided herein can exhibit upregulation of oneor more genes related to lipid biosynthesis including but not limited todesaturases, elongases, lipid droplet surface protein, and/or particularlipases, acyltransferases, and glyceraldehyde-3-phosphatedehydrogenases.

A mutant as described herein can be a mutant obtained by classicalmutagenesis or can be a genetically engineered mutant. In variousembodiments, a mutant microorganism as disclosed herein has beengenerated by introducing one or more genetic constructs (one or morenucleic acid molecules) into the microorganism. In some examples, one ormore genetic constructs introduced into a microorganism are designed toattenuate expression of a native gene.

In various examples, mutants as disclosed herein can have attenuatedexpression of a fungal type Zn(2)Cys(6) transcription factor, i.e., agene encoding a polypeptide that has a Zn(2)Cys(6) domain, e.g., has anamino acid sequence encoding a cd00067 “GAL4” domain or a “Zn_clus”domain belonging to pfam PF00172. For example, a mutant microorganismsuch as any disclosed herein having FAME production that is increased byat least 25% and biomass production that is reduced by no more than 50%with respect to a control microorganism for at least 3, at least 5, atleast 7, at least 10, at least 12, at least 13, at least 15, at least20, at least 25, or at least 30 days of culturing can have attenuatedexpression of a gene encoding a polypeptide that recruits to pfamPF00172. Alternatively or in addition, a mutant microorganism such asany disclosed herein having a FAME/TOC ratio that is at least 30% higherthan the FAME/TOC ratio of a control microorganism under conditions inwhich the control microorganism is producing biomass can be a mutantmicroorganism that has attenuated expression of a gene encoding apolypeptide having a Zn(2)Cys(6) domain, e.g., having an amino acidsequence encoding a domain belonging to pfam PF00172 or characterized asa cd00067 “GLA4” domain. In some examples, the Zn(2)Cys(6) domain canhave at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, or at least 95% identity to SEQ IDNO:3.

Thus, another aspect of the invention is mutant microorganism havingattenuated expression of a gene encoding a polypeptide having aZn(2)Cys(6) domain, wherein the mutant microorganism has increasedpartitioning of carbon to lipid with respect to a control microorganismthat does not have attenuated expression of the gene encoding apolypeptide having a ZnCys domain. For example, a mutant microorganismas provided herein having attenuated expression of a polypeptide havinga Zn(2)Cys(6) domain can have an increased FAME/TOC ratio with respectto a control cell when the mutant microorganism and controlmicroorganism are cultured under identical conditions under which thecontrol microorganism culture experiences an increase in TOC. In someexamples, a mutant microorganism as provided herein can have a FAME/TOCratio that is increased by at least 30%, at least 40%, at least 50%, atleast 60%, at least 70%, at least 80%, at least 90%, at least 100%, atleast 110%, at least 120%, at least 130%, at least 140%, or at least150% as compared to the FAME/TOC ratio of a control microorganism whenthe mutant microorganism and control microorganism are cultured underidentical conditions under which the control microorganism cultureexperiences an increase in TOC. Alternatively or in addition, a mutantmicroorganism as provided herein having attenuated expression of a geneencoding a polypeptide having a Zn(2)Cys(6) domain can have increasedproduction of FAME lipids with respect to a control microorganism whiledemonstrating no more than a 45% reduction in TOC production withrespect to the control microorganism when the mutant microorganism andcontrol microorganism are cultured under identical conditions underwhich the control microorganism experiences an increase in TOC. Forexample, a mutant microorganism as provided herein having attenuatedexpression of a gene encoding a polypeptide having a Zn(2)Cys(6) domaincan produce at least 25% or at least 50% more FAME lipids or at least75% more FAME lipids with respect to a control microorganism whiledemonstrating no more than a 50% reduction in TOC production withrespect to the control microorganism when the mutant microorganism andcontrol microorganism are cultured under identical conditions underwhich the control microorganism experiences an increase in TOC. Invarious embodiments the mutant microorganism can display higher lipidproductivity and/or carbon partitioning to lipid over a culture periodof at least 3, at least 5, at least 7, at least 10, at least 12 days, atleast 13, at least 15, at least 20, or at least 30 days. For example,mutant microorganism can have higher lipid productivity each day of theat least 5, at least 7, at least 10, at least 12 days, at least 15, atleast 20, or at least 30-day culture period.

In some exemplary embodiments the amino acid sequence of the polypeptidehaving a Zn(2)Cys(6) domain is at least 50%, at least 55%, at least 60%,at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, or at least 95% identical to any of SEQ ID NO:2, SEQ ID NO:5,SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ IDNO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ IDNO:16, or SEQ ID NO:17. In some examples, a mutant microorganism asprovided herein can have attenuated expression of a gene encoding apolypeptide having at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, or at least 95% identityto SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, or SEQ ID NO:17.For example, a mutant microorganism as provided herein can haveattenuated expression of a gene encoding a polypeptide having at least60%, at least 65%, at least 70%, at least 75%, at least 80%, at least85%, at least 90%, or at least 95% identity to SEQ ID NO:2 or SEQ IDNO:17, or at least the N-terminal 517 amino acids of SEQ ID NO:2 or theN-terminal 540 amino acids of SEQ ID NO:17. In further examples a mutantmicroorganism as provided herein has attenuated expression of a geneencoding a polypeptide that includes an amino acid sequence having atleast 55%, at least 60%, at least 65%, at least 70%, at least 75%, atleast 80%, at least 85%, at least 90%, or at least 95% identity to anyof SEQ ID NO:2, SEQ ID NO:17, SEQ ID NO:18, or SEQ ID NO:19, or to aminoacids 1-200 of SEQ ID NO:20. In some examples, a mutant microorganism asprovided herein can have attenuated expression of a gene encoding apolypeptide having at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, or at least 95% identityto SEQ ID NO:2 or SEQ ID NO:17. Alternatively or in addition, a mutantmicroorganism as provided herein can have attenuated expression of agene having a coding sequence with at least 50%, at least 55%, at least60%, at least 65%, at least 70%, at least 75%, at least 80%, at least85%, at least 90%, or at least 95% identity to SEQ ID NO:1 or any of SEQID NOs:72-84. In various embodiments the microorganism is a diatom oreustigmatophyte alga, and in some examples may be a species ofNannochloropsis.

Alternatively or in addition to any of the above, a mutant microorganismas provided herein can have attenuated expression of a gene encoding apolypeptide that has a Zn(2)Cys(6) domain and further includes a PAS3domain. In some examples the PAS3 domain comprises an amino acidsequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, orat least 95% identity to any of SEQ ID NOs:21-25. The gene whoseexpression is attenuated can additionally encoding a polypeptide thatfurther includes an amino acid sequence having at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, or at least 95% identity to at least200 amino acids of any of SEQ ID NOs:18-20.

An attenuated gene encoding a polypeptide having a Zn(2)Cys(6) domaincan be a gene that has an insertion, deletion, and/or one or more basechanges with respect to the wild type gene. The insertion, deletion, orone or more base changes can be in a coding region, intron, 3′untranslated region, or 5′ untranslated region of the gene, or can beupstream of the 5′ untranslated region of the gene, e.g., in thepromoter region of a gene, where the mutant produces less of an RNAcorresponding to the gene and/or produces less of the encodedpolypeptide. Alternatively or in addition, a mutant microorganism asprovided herein can include an antisense construct, an RNAi construct, aguide RNA (gRNA) as part of a CRISPR system, or a ribozyme that targetsthe gene encoding the polypeptide having a Zn(2)Cys(6) domain, resultingin reduced expression of the gene.

A mutant microorganism as provided herein can be any eukaryoticmicroorganism, and in some examples is a heterokont or alga. Forexample, the mutant microorganism can be a Labyrinthulomycte species,such as, for example, a species of Labryinthula, Labryinthuloides,Thraustochytrium, Schizochytrium, Aplanochytrium, Aurantiochytrium,Oblongichytrium, Japonochytrium, Diplophrys, or Ulkenia. Alternatively amutant microorganism can be an algal species such as for example, aspecies belonging to any of the genera Achnanthes, Amphiprora, Amphora,Ankistrodesmus, Asteromonas, Boekelovia, Bolidomonas, Borodinella,Botrydium, Botryococcus, Bracteococcus, Chaetoceros, Carteria,Chlamydomonas, Chlorococcum, Chlorogonium, Chlorella, Chroomonas,Chrysosphaera, Cricosphaera, Crypthecodinium, Cryptomonas, Cyclotella,Desmodesmus, Dunaliella, Elipsoidon, Emiliania, Eremosphaera,Ernodesmius, Euglena, Eustigmatos, Franceia, Fragilaria, Fragilaropsis,Gloeothamnion, Haematococcus, Hantzschia, Heterosigma, Hymenomonas,Isochrysis, Lepocinclis, Micractinium, Monodus, Monoraphidium,Nannochloris, Nannochloropsis, Navicula, Neochloris, Nephrochloris,Nephroselmis, Nitzschia, Ochromonas, Oedogonium, Oocystis, Ostreococcus,Parachlorella, Parietochloris, Pascheria, Pavlova, Pelagomonas,Phceodactylum, Phagus, Picochlorum, Platymonas, Pleurochrysis,Pleurococcus, Prototheca, Pseudochlorella, Pseudoneochloris,Pseudostaurastrum, Pyramimonas, Pyrobotrys, Scenedesmus,Schizochlamydella, Skeletonema, Spyrogyra, Stichococcus, Tetrachlorella,Tetraselmis, Thalassiosira, Tribonema, Vaucheria, Viridiella, Vischeria,and Volvox. In some embodiments a mutant microorganism is a diatom oreustigmatophyte alga. In some embodiments the mutant microorganism is aspecies of Nannochloropsis.

A further aspect of the invention is a method of producing lipid,comprising culturing a mutant microorganism as provided herein andisolating lipid from the microorganism, the culture medium, or both. Themutant microorganism can be cultured in a medium that comprises lessthan about 5 mM ammonium, less than about 2.5 mM ammonium, less than orequal to about 1 mM ammonium, or less than or equal to about 0.5 mM. Theculture medium can include, for example, from about 0 to about 2.5 mMammonium, from about 0.1 to about 2.5 mM ammonium, from about 0.5 toabout 2.5 mM ammonium, from about 0 to about 1 mM ammonium, from about0.1 to about 1 mM ammonium, or from about 0.2 to about 1 mM ammonium.The microorganism can be cultured in a medium that includes nitrate,which in some examples may be substantially the sole nitrogen source inthe culture medium or may be present in addition to ammonium that may bepresent at a concentration of less than 5 mM, less than 2.5 mM, lessthan 2 mM, or less than 1 mM. Alternatively or in addition, the culturemedium can comprise urea, which in some examples can be substantiallythe sole source of nitrogen in the culture medium. The mutantmicroorganism can be cultured under batch, continuous, orsemi-continuous mode. The mutant microorganism can in some embodimentsbe a photosynthetic microorganism, e.g., and alga, and can be culturedphotoautotrophically.

Yet another aspect of the invention is a method of producing lipid thatincludes culturing a microorganism under conditions in which the FAME toTOC ratio of the microorganism is maintained between about 0.3 and about0.8, and isolating lipid from the microorganism, the culture medium, orboth. For example, the microorganisms can be cultured such that the FAMEto TOC ratio is maintained at between about 0.3 and about 0.8, betweenabout 0.4 and about 0.7, between about 0.4 and about 0.6, or betweenabout 0.45 and about 0.55. The ratio can be maintained at between about0.3 and about 0.8, for example between about 0.4 and about 0.8, betweenabout 0.4 and about 0.7, between about 0.4 and about 0.6, or betweenabout 0.45 and about 0.55 for at least 3, at least 4, at least 5, atleast 6, at least 7, at least 8, at least 9, at least 10, at least 11,at least 12, at least 13, at least 15, at least 20, at least 30 days, orat least 60 days. The microorganism can be cultured under batch,continuous, or semi-continuous mode. The method of producing lipid caninclude culturing a mutant microorganism such as any provided hereinunder conditions in which the FAME to TOC ratio of the microorganism ismaintained between about 0.3 and about 0.8, between about 0.3 and about0.8, between about 0.4 and about 0.7, between about 0.4 and about 0.6,or between about 0.45 and about 0.55. For example, the microorganism canbe a mutant microorganism having attenuated expression of a Zn(2)Cys(6)regulator gene, such as but not limited to a gene encoding a polypeptidehaving at least 55%, at least 65%, at least 75%, or at least 85%identity to a polypeptide comprising an amino acid sequence selectedfrom the group consisting of SEQ ID NO:2 and SEQ ID NOs:5-17.Alternatively or in addition, the microorganism can be a mutantmicroorganism having attenuated expression of a gene that has a codingsequence having at least 50%, at least 55%, at least 60%, least 65%, atleast 70%, at least 75%, at least 80%, at least 85% at least 90%, or atleast 95% identity to SEQ ID NO:1 or any of SEQ ID NOs:71-84. In any ofthe above methods for producing lipid, the mutant microorganism can bean alga, and the culturing can be under photoautotrophic conditions,i.e., conditions in which inorganic carbon is substantially the solecarbon source in the culture medium.

Yet another aspect of the invention is a nucleic acid moleculecomprising a nucleic acid sequence encoding a polypeptide including anamino acid sequence having at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, or at least 75%, at least 80%, at least 85%, atleast 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ IDNO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11,SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, orSEQ ID NO:17. The polypeptide having at least 60% identity to a nucleicacid sequence selected from the group consisting of SEQ ID NO:2 and SEQID NOs:5-17 can include an amino acid sequence encoding a Zn(2)Cys(6)domain. The nucleic acid molecule in various examples can be or comprisea cDNA that lacks one or more introns present in the naturally-occurringgene, or, alternatively, can include one or more introns not present inthe naturally-occurring gene. The nucleic acid molecule in variousexamples can have a sequence that is not 100% identical to anaturally-occurring gene. The nucleic acid molecule in various examplescan comprise a heterologous promoter operably linked to the sequenceencoding a polypeptide that includes an amino acid sequence having atleast 50%, at least 55%, at least 60%, at least 65%, at least 70%, or atleast 75%, at least 80%, at least 85%, at least 90%, or at least 95%identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ IDNO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ IDNO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17 and/orcan comprise a vector that includes a sequence encoding a polypeptidethat includes an amino acid sequence having at least 50%, at least 55%,at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%,at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ IDNO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ IDNO:15, SEQ ID NO:16, or SEQ ID NO:17.

A further aspect of the invention is a construct designed forattenuating expression of a gene encoding a polypeptide containing aZn(2)Cys(6) domain. The construct can be or comprise, in variousexamples, a sequence encoding a guide RNA of a CRISPR system, an RNAiconstruct, an antisense construct, a ribozyme construct, or a constructfor homologous recombination, e.g., a construct having one or morenucleotide sequences having homology to a naturally-occurringZn(2)Cys(6) domain-encoding gene as disclosed herein and/or sequencesadjacent thereto in the native genome from which the gene is derived.For example, the construct can include at least a portion of a geneencoding a polypeptide having a Zn(2)Cys(6) domain, e.g., a sequencehomologous to at least a portion of an gene that encodes a polypeptidethat includes an amino acid sequence having at least 50%, at least 55%,at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%,at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQID NO:3, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ IDNO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ IDNO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17. Alternatively or inaddition, the construct can include a sequence having at least 50%, atleast 55%, at least 60%, least 65%, at least 70%, at least 75%, at least80%, at least 85% at least 90%, or at least 95% identity to SEQ ID NO:1or any of SEQ ID NOs:71-84.

The construct can include, for example, at least a portion of the codingregion of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, atleast a portion of an intron of a gene encoding a polypeptide having aZn(2)Cys(6) domain, at least a portion of a 5′UTR of a gene encoding apolypeptide having a Zn(2)Cys(6) domain, at least a portion of thepromoter region of a gene encoding a polypeptide having a Zn(2)Cys(6)domain, and/or at least a portion of a 3′ UTR of a gene encoding apolypeptide having a Zn(2)Cys(6) domain. In some examples, the constructcan be an RNAi, ribozyme, or antisense construct and can include asequence from the transcribed region of the gene encoding a polypeptidehaving a Zn(2)Cys(6) domain in either sense or antisense orientation. Infurther examples a construct can be designed for the in vitro or in vivoexpression of a guide RNA (e.g., of a CRISPR system) designed to targeta gene encoding a polypeptide having a Zn(2)Cys(6) domain, and caninclude a sequence homologous to a portion of a gene encoding apolypeptide having a Zn(2)Cys(6) domain, including, for example, anintron, a 5′UTR, a promoter region, and/or a 3′ UTR of a gene encoding apolypeptide having a Zn(2)Cys(6) domain. In yet further examples, aconstruct for attenuating expression a gene encoding a Zn(2)Cys(6)domain-containing polypeptide can be a guide RNA of a CRISPR system or aCRISPRi system or can be an antisense oligonucleotide, where thesequence having homology to a transcribed region of a gene encoding apolypeptide having a Zn(2)Cys(6) domain is in antisense orientation.

These and other objects and features of the invention will become morefully apparent when the following detailed description of the inventionis read in conjunction with the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A provides a graph showing lipid (FAME) accumulation of wild-typeNannochloropsis cultures grown in N replete (+N) and deplete (−N)conditions. The 3-hour time point samples were subjected totranscriptomic analysis (RNA-seq). FIG. 1B provides a plot of thedifferentially expressed genes in cells transferred to −N mediumcompared to cells provided with N replete medium. The genes (representedas dots) are plotted versus fold change (log₂) in −N treated cellscompared to replete cells. Putative transcription factors arerepresented as Xs. Genes present in the right side of the y-axis areupregulated and genes on the left side of the y-axis are downregulated.Only genes with a false discovery rate (FDR) less than or equal to 0.01are displayed on the graph.

FIG. 2 is a schematic map of vector pSGE-6206 used to introduce the Cas9gene into the N. gaditana Editor line.

FIG. 3A provides a map of the vector used in to generate the Cas9expression strain Ng-CAS9+ in Nannochloropsis. FIG. 3B is an overlayedhistogram from the Accuri C6 flow cytometer showing GFP fluorescence inthe Ng-Cas9 editor strain (right peak, in red) compared to the wild typestrain (left peak, in black). FIG. 3C is an image of a western blot withan anti-FLAG antibody demonstrating Cas9 expression in the Ng-CAS9+line, with no background in the wild type control.

FIG. 4A provides a diagram of the donor fragment used for genedisruption at Cas9 target sites. The donor fragment construct includesthe HygR (hygromycin resistance) gene driven by the EIF3 promoter andfollowed by the GNPDA terminator in inverted orientation. FIG. 4B is aschematic representation of a Cas9-mediated insertion of the hygromycinresistance (HygR) cassette into the ZnCys locus. The HygR cassetteconsisted of a promoter (Prom) driving the HygR gene followed by aterminator (T). The resulting mutant genotype (ZnCys-KO) was identifiedby PCR using primers that flank the insertion (arrows). The diagram isnot to scale. FIG. 4C shows PCR genotyping of several Hyg resistantcolonies transformed with a guide RNA designed to target the ZnCyslocus. Presence of a 3 Kb band indicates insertion into the intendedlocus, while a 0.5 Kb band indicates an intact wild-type locus.

FIG. 5 is a schematic depiction of the N. gaditana ZnCys-2845 gene. Abox denotes the position of the Zn(2)Cys(6) domain, which was the regiontargeted by the RNAi construct. Positions of insertions of the donorfragment in the BASH-3, knockout, and BASH-12 mutants are shown byarrows. The general location of the putative monopartite nuclearlocalization signal is also shown (NLS). The figure is not to scale.

FIG. 6A provides incident irradiance profiles for batch growthassessment and FIG. 6B is the Semi-continuous Productivity Assay.

FIG. 7A is a graph depicting FAME productivity of wild-type andZnCys-2845 knockout N. gaditana cells cultured in batch mode innitrate-only medium as determined from samples taken on odd days of theculture. FIG. 7B is a graph depicting TOC productivities for days 3-7 ofthe batch productivity assay. FIG. 7C is a graph depicting FAME/TOCratios calculated from samples taken on odd days of the culture. FIG. 7Dis a bar graph depicting the amount of fatty acids of various chainlengths present in the lipid isolated on day 7 of the batch assay fromwild type WT-3730 and ZnCys 2845 knockout strain GE-8564. FIG. 7E is abar graph depicting the level of TAG isolated from wild type and ZnCys2845 knockout strain GE-8564 on day 7 of the batch assay. FIG. 7F is anelectron micrograph of a wild type Nannochloropsis gaditana cellcultured in nitrate-only (nitrogen-replete) culture medium. FIG. 7G isan electron micrograph of a Nannochloropsis gaditana ZnCys knockoutmutant GE-8564 cell cultured in nitrate-only culture medium. FIG. 7H isan electron micrograph of a wild type Nannochloropsis gaditana cellcultured in nitrogen-deplete culture medium. Error bars in graphsrepresent the standard deviation for the average value of three cultures(biological replicates). Symbols used in graphs: asterisks representwild type WT-3730 cultured in nitrate plus ammonium medium PM124, blackdiamonds represent knockout mutant GE-8564 cultured in nitrate plusammonium medium PM124, X's represent wild type WT-3730 cultured innitrate-only medium PM074, and black circles represent knockout mutantGE-8564 cultured in nitrate-only medium PM074. N: nucleus; Ch:chloroplast; LD: lipid droplet; M: mitochondrion.

FIGS. 8A-8B provide graphs demonstrating repression of the lipidaccumulation phenotype of ZnCys-KO by NH₄ ⁺ supplementation in afive-day batch mode assay. FIG. 8A shows FAME (mg/L) per day. FIG. 8Bshows TOC (mg/L) per day. FIG. 8C shows FAME/TOC values per day ofZnCys-KO (circles) and WT (diamonds) grown in batch mode on mediumsupplemented with NH₄ ⁺ (SM-NH₄ ⁺/NO₃ ⁻). Error bars are standarddeviations of 2 biological replicates (n=2).

FIG. 9 is an alignment of the PAS3 domain sequences of N. gaditanaZnCys-2845 and the PAS3 domain sequences of the ZnCys-2845 orthologs ofN. oceanica, N. oculata, N. salina, and N. granulata.

FIG. 10 is an alignment of the N. gaditana polypeptide sequence encodedby the ZnCys-2845 gene and the N. oceanica polypeptide sequence encodedby the ortholog of the ZnCys-2845 gene, as well as partial N-terminalsequences of polypeptides encoded by orthologous genes in N. granulata,N. oculata, and N. salina.

FIGS. 11A-11C provide graphs depicting productivities of the N. gaditanawild type strain and GE-8564 knockout strain in a semi-continuous assayin which the culture medium includes urea as the sole nitrogen source.FIG. 11A shows daily FAME productivity over thirteen days of the assay.FIG. 11B shows daily TOC productivity over thirteen days of the assay.FIG. 11C) provides the FAME/TOC ratios for each day of the assay. Errorbars in graphs represent the standard deviation of the three independentcultures (biological replicates). Symbols used in graphs: squaresrepresent wild type WT-3730 cultured in urea-only medium PM125,triangles represent wild type WT-3730 cultured in nitrate-only mediumPM074, circles represent ZnCys-2845 knockout mutant GE-8564 cultured inurea-only medium PM125, and diamonds represent ZnCys-2845 knockoutmutant GE-8564 cultured in nitrate-only medium PM074.

FIG. 12A is a schematic depiction of the ZnCys-2845 gene with thepositions of the nuclear localization signal (NLS), Zn(2)Cys(6) domain(Zn) and PAS3 domain shown as boxes and arrows depicting the sites ofCRISPR-targeted mutations. FIG. 12B shows the relative transcript levelsof the corresponding CRISPR-targeted mutants (position of primers usedfor transcript assessment shown in FIG. 12A. Normalized expressionlevels are relative to the average wild type level which was set to 1.0.

FIG. 13A is a graph depicting FAME productivity of wild-type andZnCys-2845 knockdown N. gaditana cells cultured in batch mode innitrate-only medium. FIG. 13B is a graph depicting TOC values for theodd days of the screen (days 1-3 and days 3-5). FIG. 13C is a graphproviding FAME/TOC ratios of the cultures calculated on days 3, 5, and7. Symbols used in graphs: open circles represent wild type WT-3730, aplus sign represents knockout mutant GE-13108, “BASH2”; an asteriskrepresents knockout mutant GE-13109, “BASH3”; Xs represent knockoutmutant GE-13112, “BASH12”; open triangles represent ZnCys-2845 knockoutmutant GE-8564; and dashes represent RNAi-7 strain GE-13103. The Errorbars represent the standard deviation of two calculated productivityvalues of two separate cultures.

FIG. 14A provides the modular structure and salient features of theZnCys locus. Abbreviations: NLS, nuclear localization sequence; Zn₂Cys₆,Zn(II)2Cys6 binuclear cluster domain (Pfam id: PF00172). The approximatelocation of the insertion in the original ZnCys-KO mutant is indicatedwith a black arrow. Patterned arrows indicate locations of successfulCas9 insertional mutants in putative 5′UTR (BASH-3 (strain GE-13109) ˜65bp from the predicted start site) and 3′UTR regions (BASH-12 (strainGE-13112), approximately 30 bp from the predicted stop codon). Blackhorizontal arrows show the approximate location of the qRT-PCR primersused for assessing gene expression levels in panel B. The RNAi hairpindesigned to silence ZnCys spanned the conserved Zn₂Cys₆ domain washomologous to the sequence denoted by the dotted double arrow. Thefigure is not to scale. FIG. 14B shows steady-state mRNA levels of theZnCys locus in attenuated ZnCys lines (left to right on graph, wild type(WT) ZnCys-BASH-3, ZnCys-BASH-12, ZnCys-RNAi-7, and ZnCys-KO) relativeto wild type (WT) as determined by qRT-PCR (left to right on graph, wildtype (WT) ZnCys-BASH-3, ZnCys-BASH-12, ZnCys-RNAi-7, and ZnCys-KO).Expression levels were normalized to a housekeeping gene and werecalculated relative to WT using the ΔΔC_(T) method. Error bars arestandard errors for 3 technical replicates. FIG. 14C shows TOCproductivity and FAME/TOC values of ZnCys mutant lines assessed in batchmode in nitrate-replete medium (SM-NO3-). Individual data points used tocalculate FAME/TOC and biomass productivity averages are shown in FIGS.15A-15B. Error bars are standard deviations of two biologicalreplicates.

FIG. 15A is a batch mode assessment of FAME (mg/L) produced by ZnCysattenuated lines (ZnCys-BASH-3 (GE-13109), ZnCys-BASH-12 (GE-13112),ZnCys-RNAi-7 (GE-13103)) grown in nitrate-replete medium. FIG. 15B is abatch mode assessment of TOC (mg/L) measurements corresponding to days3, 5 and 7 of the screen.

FIGS. 16A-16D provide graphs and a table depicting productivities of theN. gaditana wild type strain and GE-8564 knockout strain in asemi-continuous assay in which the culture medium used for dailydilution includes nitrate as the sole nitrogen source. FIG. 16A showsdaily FAME productivity over thirteen days of the assay (mg/L culture).FIG. 16B provides the daily productivities of the cultures in g/m2/day(standard deviation of three cultures provided in parentheses), alongwith the average daily productivity for each culture. FIG. 16C showsdaily TOC productivity over thirteen days of the assay (mg/L culture).FIG. 16D provides the FAME/TOC ratios for each day of the assay Symbolsused in graphs: diamonds represent wild type WT-3730 pre-cultured innitrate-only medium; Xs represent knockdown mutant GE-13108 “BASH2”pre-cultured in nitrate plus ammonium medium; triangles representknockdown mutant GE-13109 “BASH3” pre-cultured in nitrate plus ammoniummedium; squares represent knockdown mutant GE-13112 “BASH12”pre-cultured in nitrate plus ammonium medium; open circles representknockdown mutant GE-13103 “RNAi-7” pre-cultured in nitrate plus ammoniummedium; closed circles represent knockdown mutant GE-13103 “RNAi-7”pre-cultured in nitrate-only medium; and dashes represent knockoutmutant GE-8564 pre-cultured in nitrate plus ammonium medium. Error barsin graphs represent the standard deviation of the three independentcultures (biological replicates).

FIGS. 17A-17B. Productivity assessment of ZnCys mutants grown insemi-continuous mode for 8 days on NO₃ ⁻-containing culture medium. FIG.17A shows daily FAME and FIG. 17B shows TOC (mg/L) measurements forZnCys mutants (ZnCys-RNAi-7, ZnCys-BASH-12 and ZnCys-BASH-3) compared totheir parental lines Ng-CAS9+ and WT. Cultures were grown insemi-continuous mode at a 30% daily dilution rate on SM-NO₃ ⁻. Errorbars represent standard deviations for 3 biological replicates (n=3).

FIG. 18 provides a bar graph of FAME and TOC productivities (g/m²/day)of ZnCys mutants (ZnCys-RNAi-7 (GE-13103), ZnCys-BASH-12 (GE-13112) andZnCys-BASH-3 (GE-13109)) compared to their parental lines Ng-CAS9+(GE-6791) and WT in the assay whose daily FAME and TOC productivitiesare depicted in FIGS. 17A-17B. Productivity values are 8-day averages ofdaily measurements (n=3).

FIG. 19 provides a graph depicting the daily nitrogen content of thecells (mg/L culture, pellets only) in the semi-continuous assay whosedaily FAME and TOC productivities are provided in FIGS. 16A-16D. Symbolsused in graphs: diamonds represent wild type WT-3730 pre-cultured innitrate-only medium; Xs represent knockdown mutant GE-13108 “BASH2”pre-cultured in nitrate plus ammonium medium; triangles representknockdown mutant GE-13109 “BASH3” pre-cultured in nitrate plus ammoniummedium; squares represent knockdown mutant GE-13112 “BASH12”pre-cultured in nitrate plus ammonium medium; open circles representknockdown mutant GE-13103 “RNAi-7” pre-cultured in nitrate plus ammoniummedium; closed circles represent knockdown mutant GE-13103 “RNAi-7”pre-cultured in nitrate-only medium; and dashes represent knockoutmutant GE-8564 pre-cultured in nitrate plus ammonium medium. Error barsin graphs represent the standard deviation of the three independentcultures (biological replicates).

FIG. 20 provides a graph depicting total nitrogen and FAME levels ofcultures of N. gaditana wild type strain WT-3730 and RNAi mutantGE-13103 in a semi-continuous assay using nitrate-only media, in whichthe GE-13103 knockdown strain was pre-cultured separately in eitherPM124 medium that included both nitrate and ammonium or in PM074 mediumthat included only nitrate. Wild type strain WT-3730 was pre-cultured inPM074 medium that included only nitrate. Solid diamonds and solidtriangles represent the total nitrogen content of the cultures (cellsplus culture medium) of GE-13103 pre-cultured in PM124 and PM074,respectively. Open diamonds and open triangles represent the FAMEcontent of the cultures of GE-13103 pre-cultured in PM124 and PM074,respectively. Solid squares represent the FAME content of a culture ofWT-3730 pre-cultured in nitrate-only medium. The calculated amount ofammonium on three days of the productivity assay is noted on the graph.

FIGS. 21A-21F provides graphs and a table depicting productivities ofthe N. gaditana wild type strain WT-3730 and GE-13103 knockdown strainin a semi-continuous assay in which the culture medium included threedifferent concentrations of ammonium. FIG. 21A depicts FAME productivity(mg/L) in the semi-continuous assay in culture in which the ammoniumlevel of the media used throughout the assay was 2.5, 1.0, or 0.5 mM.FIG. 21B provides daily FAME productivities (g/m²/day) (standarddeviation of three cultures provided in parentheses), along with theaverage daily productivity for each culture condition in thesemi-continuous assay in which the ammonium level of the media usedthroughout the assay was 2.5, 1.0, or 0.5 mM. FIG. 21C depicts TOCproductivity (mg/L) in the semi-continuous assay in which the ammoniumlevel of the media used throughout the assay was 2.5, 1.0, or 0.5 mM.FIG. 21D provides daily TOC productivities (g/m²/day) (standarddeviation of three cultures for each ammonium concentration provided inparentheses), along with the average daily productivity for each culturecondition in the semi-continuous assay in which the ammonium level ofthe media used throughout the assay was 2.5, 1.0, or 0.5 mM. FIG. 21Edepicts daily FAME/TOC ratios in the semi-continuous assay in which theammonium level of the media used throughout the assay was 2.5, 1.0, or0.5 mM. FIG. 21F provides daily cell counts determined by flow cytometryof cultures analyzed for FAME and TOC productivities in FIGS. 21A-21E.Symbols used in graphs: Circles: WT-3730 cultured in nitrate-onlymedium; Squares: RNAi knockdown strain GE-13103 cultured innitrate-containing medium that also included 2.5 mM ammonium; Triangles:RNAi knockdown strain GE-13103 cultured in nitrate-containing mediumthat also included 1.0 mM ammonium; Xs: RNAi knockdown strain GE-13103cultured in nitrate-containing medium that also included 0.5 mMammonium. Error bars in graphs represent the standard deviation of thethree independent cultures (biological replicates).

FIGS. 22A-22E. Productivity assessment of ZnCys-KO and ZnCys-RNAi-7grown in semi-continuous mode on nitrate-containing medium. FIG. 22Adepicts daily FAME (mg/L). FIG. 22B depicts daily TOC (mg/L). FIG. 22Cdepicts C/N values derived from cellular N-content. FIG. 22D provides abar graph comparing FAME. FIG. 22E depicts TOC productivities (g/m²/day)for WT and ZnCys-RNAi-7 calculated for the entire 13-day assay. ZnCys-KOfailed to reach steady-state at a 30% daily dilution scheme andessentially washed away as the run progressed, therefore lipid andbiomass productivity values were not calculated for this line (N/A, notavailable). ZnCys-KO was scaled up in culture medium that included NH₄ ⁺in addition to NO₃ ⁻ to obtain enough biomass for the assay.

FIG. 23 is a bar graph depicting the biomolecular composition of wildtype Nannochloropsis strain WT-3730 and two ZnCys knockdown mutants,GE-13112 (BASH 12) and GE-13130 (RNAi).

FIG. 24 depicts hierarchical clustering by Euclidian distance oftranscriptional fold changes of genes encoding proteins involved inN-assimilation from biological triplicates of ZnCys-KO, the nitratereductase knockout mutant (NR-KO), RNAi-7 and WT grown in batch mode onnitrate-only medium (NO₃, light green) or medium that included bothammonium and nitrate (NH₄, dark green). Red indicates increasedexpression and blue indicates reduced expression, with black beingneutral (neither increased nor decreased).

FIG. 25 provides images of immunoblot analysis of enzymes in the FAScycle (KAR1, KAS1/3, HAD and ENR), acetyl-CoA carboxylase (ACCase),glutamate synthase (GOGAT2) and nitrate reductase (NR) for duplicatecultures grown in batch mode on nitrate-only medium (WT, ZnCys-KO andZnCys-RNAi-7 shown as RNAi-7). Coomassie brilliant blue stain (CBB) of aprotein gel used for blotting is shown as a loading reference.

DETAILED DESCRIPTION OF THE INVENTION Definitions

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. In case of conflict, thepresent application including the definitions will control. Unlessotherwise required by context, singular terms shall include pluralitiesand plural terms shall include the singular. All ranges provided withinthe application are inclusive of the values of the upper and lower endsof the range unless specifically indicated otherwise.

All publications, patents and other references mentioned herein areincorporated by reference in their entireties for all purposes as ifeach individual publication or patent application were specifically andindividually indicated to be incorporated by reference.

The term “and/or” as used in a phrase such as “A and/or B” herein isintended to include “A and B”, “A or B”, “A”, and “B”.

“About” means either within 10% of the stated value, or within 5% of thestated value, or in some cases within 2.5% of the stated value, or,“about” can mean rounded to the nearest significant digit.

The term “gene” is used broadly to refer to any segment of a nucleicacid molecule (typically DNA, but optionally RNA) encoding a polypeptideor expressed RNA. Thus, genes include sequences encoding expressed RNA(which can include polypeptide coding sequences or, for example,functional RNAs, such as ribosomal RNAs, tRNAs, antisense RNAs,microRNAs, short hairpin RNAs, ribozymes, etc.). Genes may furthercomprise regulatory sequences required for or affecting theirexpression, as well as sequences associated with the protein orRNA-encoding sequence in its natural state, such as, for example, intronsequences, 5′ or 3′ untranslated sequences, etc. In some examples,“gene” may only refer to a protein-encoding portion of a DNA or RNAmolecule, which may or may not include introns. A gene is preferablygreater than 50 nucleotides in length, more preferably greater than 100nucleotides in length, and can be, for example, between 50 nucleotidesand 500,000 nucleotides in length, such as between 100 nucleotides and100,000 nucleotides in length or between about 200 nucleotides and about50,000 nucleotides in length, or about 200 nucleotides and about 20,000nucleotides in length. Genes can be obtained from a variety of sources,including cloning from a source of interest or synthesizing from knownor predicted sequence information.

The term “nucleic acid” or “nucleic acid molecule” refers to, a segmentof DNA or RNA (e.g., mRNA), and also includes nucleic acids havingmodified backbones (e.g., peptide nucleic acids, locked nucleic acids)or modified or non-naturally-occurring nucleobases. The nucleic acidmolecules can be double-stranded or single-stranded; a single strandednucleic acid molecule that comprises a gene or a portion thereof can bea coding (sense) strand or a non-coding (antisense) strand.

A nucleic acid molecule may be “derived from” an indicated source, whichincludes the isolation (in whole or in part) of a nucleic acid segmentfrom an indicated source. A nucleic acid molecule may also be derivedfrom an indicated source by, for example, direct cloning, PCRamplification, or artificial synthesis from the indicated polynucleotidesource or based on a sequence associated with the indicatedpolynucleotide source, which may be, for example, a species of organism.Genes or nucleic acid molecules derived from a particular source orspecies also include genes or nucleic acid molecules having sequencemodifications with respect to the source nucleic acid molecules. Forexample, a gene or nucleic acid molecule derived from a source (e.g., aparticular referenced gene) can include one or more mutations withrespect to the source gene or nucleic acid molecule that are unintendedor that are deliberately introduced, and if one or more mutations,including substitutions, deletions, or insertions, are deliberatelyintroduced the sequence alterations can be introduced by random ortargeted mutation of cells or nucleic acids, by amplification or othergene synthesis or molecular biology techniques, or by chemicalsynthesis, or any combination thereof. A gene or nucleic acid moleculethat is derived from a referenced gene or nucleic acid molecule thatencodes a functional RNA or polypeptide can encode a functional RNA orpolypeptide having at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, or at least 95%, sequence identity withthe referenced or source functional RNA or polypeptide, or to afunctional fragment thereof. For example, a gene or nucleic acidmolecule that is derived from a referenced gene or nucleic acid moleculethat encodes a functional RNA or polypeptide can encode a functional RNAor polypeptide having at least 85%, at least 90%, at least 95%, at least96%, at least 97%, at least 98%, or at least 99% sequence identity withthe referenced or source functional RNA or polypeptide, or to afunctional fragment thereof.

As used herein, an “isolated” nucleic acid or protein is removed fromits natural milieu or the context in which the nucleic acid or proteinexists in nature. For example, an isolated protein or nucleic acidmolecule is removed from the cell or organism with which it isassociated in its native or natural environment. An isolated nucleicacid or protein can be, in some instances, partially or substantiallypurified, but no particular level of purification is required forisolation. Thus, for example, an isolated nucleic acid molecule can be anucleic acid sequence that has been excised from the chromosome, genome,or episome that it is integrated into in nature, or has been synthesizedapart from other sequences of the chromosome, genome, or episome that itis associated with in nature, or has been synthesized apart from othersequences with which it is juxtaposed in nature.

A “purified” nucleic acid molecule or nucleotide sequence, or protein orpolypeptide sequence, is substantially free of cellular material andcellular components. The purified nucleic acid molecule or protein maybe substantially free of chemicals beyond buffer or solvent, forexample. “Substantially free” is not intended to mean that othercomponents beyond the novel nucleic acid molecules are undetectable.

The terms “naturally-occurring” and “wild type” refer to a form found innature. For example, a naturally occurring or wild type nucleic acidmolecule, nucleotide sequence or protein may be present in and isolatedfrom a natural source, and is not intentionally modified by humanmanipulation.

As used herein “attenuated” means reduced in amount, degree, intensity,or strength with respect to a control that does not have themanipulation or mutation that results in attenuated expression oractivity. Attenuated gene expression may refer to a significantlyreduced amount and/or rate of transcription of the gene in question, orof translation, folding, or assembly of the encoded protein. Asnonlimiting examples, an attenuated gene may be an endogenous gene ofthe organism that is mutated or disrupted (e.g., a gene disrupted bypartial or total deletion, truncation, frameshifting, or insertionalmutation) that does not encode a complete functional open reading frameor that has decreased expression due to alteration or disruption of generegulatory sequences. An attenuated gene may also be a gene targeted bya construct that reduces expression of the gene, such as, for example,an antisense RNA, microRNA, RNAi molecule, or ribozyme. Attenuated geneexpression can be gene expression that is eliminated, for example,reduced to an amount that is insignificant or undetectable, or can begene expression the is reduced by any amount with respect to the geneexpression of a control microorganism, for example reduced from about 1%to about 99%, or from about 5% to about 95% of the level of geneexpression of the control microorganism. Attenuated gene expression canalso be gene expression that results in an RNA or protein that is notfully functional or nonfunctional, for example, attenuated geneexpression can be gene expression that results in a truncated RNA and/orpolypeptide.

“Exogenous nucleic acid molecule” or “exogenous gene” refers to anucleic acid molecule or gene that has been introduced (“transformed”)into a cell. A transformed cell may be referred to as a recombinantcell, into which additional exogenous gene(s) may be introduced. Adescendent of a cell transformed with a nucleic acid molecule is alsoreferred to as “transformed” if it has inherited the exogenous nucleicacid molecule. The exogenous gene may be from a different species (andso “heterologous”), or from the same species (and so “homologous”),relative to the cell being transformed. An “endogenous” nucleic acidmolecule, gene or protein is a native nucleic acid molecule, gene orprotein as it occurs in, or is naturally produced by, the host.

The term “native” is used herein to refer to nucleic acid sequences oramino acid sequences as they naturally occur in the host. The term“non-native” is used herein to refer to nucleic acid sequences or aminoacid sequences that do not occur naturally in the host. A nucleic acidsequence or amino acid sequence that has been removed from a cell,subjected to laboratory manipulation, and introduced or reintroducedinto a host cell such that it differs in sequence or location in thegenome with respect to its position in a non-manipulated organism (i.e.,is juxtaposed with or operably linked to sequences it is not juxtaposedwith or operably linked to in a non-transformed organism) is considered“non-native”. Thus non-native genes include genes endogenous to the hostmicroorganism operably linked to one or more heterologous regulatorysequences that have been recombined into the host genome.

A “recombinant” or “engineered” nucleic acid molecule is a nucleic acidmolecule that has been altered through human manipulation. Asnon-limiting examples, a recombinant nucleic acid molecule includes anynucleic acid molecule that: 1) has been partially or fully synthesizedor modified in vitro, for example, using chemical or enzymatictechniques (e.g., by use of chemical nucleic acid synthesis, or by useof enzymes for the replication, polymerization, digestion(exonucleolytic or endonucleolytic), ligation, reverse transcription,transcription, base modification (including, e.g., methylation),integration or recombination (including homologous and site-specificrecombination) of nucleic acid molecules); 2) includes conjoinednucleotide sequences that are not conjoined in nature; 3) has beenengineered using molecular cloning techniques such that it lacks one ormore nucleotides with respect to the naturally occurring nucleic acidmolecule sequence; and/or 4) has been manipulated using molecularcloning techniques such that it has one or more sequence changes orrearrangements with respect to the naturally occurring nucleic acidsequence. As non-limiting examples, a cDNA is a recombinant DNAmolecule, as is any nucleic acid molecule that has been generated by invitro polymerase reaction(s), or to which linkers have been attached, orthat has been integrated into a vector, such as a cloning vector orexpression vector.

The term “recombinant protein” as used herein refers to a proteinproduced by genetic engineering regardless of whether the amino acidsequence varies from that of a wild-type protein.

When applied to organisms, the term recombinant, engineered, orgenetically engineered refers to organisms that have been manipulated byintroduction of a heterologous or exogenous recombinant nucleic acidsequence into the organism, and includes gene knockouts, targetedmutations, gene replacement, and promoter replacement, deletion, orinsertion, as well as introduction of transgenes or synthetic genes intothe organism. Recombinant or genetically engineered organisms can alsobe organisms into which constructs for gene “knockdown” have beenintroduced. Such constructs include, but are not limited to, RNAi,microRNA, shRNA, siRNA, antisense, and ribozyme constructs. Alsoincluded are organisms whose genomes have been altered by the activityof meganucleases, zinc finger nucleases, TALENs, or cas/CRISPR systems.An exogenous or recombinant nucleic acid molecule can be integrated intothe recombinant/genetically engineered organism's genome or in otherinstances may not be integrated into the host genome. As used herein,“recombinant microorganism” or “recombinant host cell” includes progenyor derivatives of the recombinant microorganisms of the invention.Because certain modifications may occur in succeeding generations due toeither mutation or environmental influences, such progeny or derivativesmay not, in fact, be identical to the parent cell, but are stillincluded within the scope of the term as used herein.

The term “promoter” refers to a nucleic acid sequence capable of bindingRNA polymerase in a cell and initiating transcription of a downstream(3′ direction) coding sequence. A promoter includes the minimum numberof bases or elements necessary to initiate transcription at levelsdetectable above background. A promoter can include a transcriptioninitiation site as well as protein binding domains (consensus sequences)responsible for the binding of RNA polymerase. Eukaryotic promotersoften, but not always, contain “TATA” boxes and “CAT” boxes. Prokaryoticpromoters may contain −10 and −35 prokaryotic promoter consensussequences. A large number of promoters, including constitutive,inducible and repressible promoters, from a variety of different sourcesare well known in the art. Representative sources include for example,algal, viral, mammalian, insect, plant, yeast, and bacterial cell types,and suitable promoters from these sources are readily available, or canbe made synthetically, based on sequences publicly available on line or,for example, from depositories such as the ATCC as well as othercommercial or individual sources. Promoters can be unidirectional(initiate transcription in one direction) or bi-directional (initiatetranscription in either direction). A promoter may be a constitutivepromoter, a repressible promoter, or an inducible promoter. A promoterregion can include, in addition to the gene-proximal promoter where RNApolymerase binds to initiate transcription, additional sequencesupstream of the gene that can be within 1 kb, 2 kb, 3 kb, 4 kb, 5 kb ormore of the transcriptional start site of a gene, where the additionalsequences can influence the rate of transcription of the downstream geneand optionally the responsiveness of the promoter to developmental,environmental, or biochemical (e.g., metabolic) conditions.

The term “heterologous” when used in reference to a polynucleotide,gene, nucleic acid, polypeptide, or enzyme refers to a polynucleotide,gene, nucleic acid, polypeptide, or enzyme that is from a source orderived from a source other than the host organism species. In contrasta “homologous” polynucleotide, gene, nucleic acid, polypeptide, orenzyme is used herein to denote a polynucleotide, gene, nucleic acid,polypeptide, or enzyme that is derived from the host organism species.When referring to a gene regulatory sequence or to an auxiliary nucleicacid sequence used for maintaining or manipulating a gene sequence(e.g., a promoter, a 5′ untranslated region, 3′ untranslated region,poly A addition sequence, intron sequence, splice site, ribosome bindingsite, internal ribosome entry sequence, genome homology region,recombination site, etc.), “heterologous” means that the regulatorysequence or auxiliary sequence is not naturally associated with the genewith which the regulatory or auxiliary nucleic acid sequence isjuxtaposed in a construct, genome, chromosome, or episome. Thus, apromoter operably linked to a gene to which it is not operably linked toin its natural state (i.e., in the genome of a non-geneticallyengineered organism) is referred to herein as a “heterologous promoter,”even though the promoter may be derived from the same species (or, insome cases, the same organism) as the gene to which it is linked.

As used herein, the term “protein” or “polypeptide” is intended toencompass a singular “polypeptide” as well as plural “polypeptides,” andrefers to a molecule composed of monomers (amino acids) linearly linkedby amide bonds (also known as peptide bonds). The term “polypeptide”refers to any chain or chains of two or more amino acids, and does notrefer to a specific length of the product. Thus, peptides, dipeptides,tripeptides, oligopeptides, “protein,” “amino acid chain,” or any otherterm used to refer to a chain or chains of two or more amino acids, areincluded within the definition of “polypeptide,” and the term“polypeptide” can be used instead of, or interchangeably with any ofthese terms.

Gene and protein Accession numbers, commonly provided in parenthesisafter a gene or species name, are unique identifiers for a sequencerecord publicly available at the National Center for BiotechnologyInformation (NCBI) website (ncbi.nlm.nih.gov) maintained by the UnitedStates National Institutes of Health. The “GenInfo Identifier” (GI)sequence identification number is specific to a nucleotide or amino acidsequence. If a sequence changes in any way, a new GI number is assigned.A Sequence Revision History tool is available to track the various GInumbers, version numbers, and update dates for sequences that appear ina specific GenBank record. Searching and obtaining nucleic acid or genesequences or protein sequences based on Accession numbers and GI numbersis well known in the arts of, e.g., cell biology, biochemistry,molecular biology, and molecular genetics.

As used herein, the terms “percent identity” or “homology” with respectto nucleic acid or polypeptide sequences are defined as the percentageof nucleotide or amino acid residues in the candidate sequence that areidentical with the known polypeptides, after aligning the sequences formaximum percent identity and introducing gaps, if necessary, to achievethe maximum percent homology. N-terminal or C-terminal insertion ordeletions shall not be construed as affecting homology, and internaldeletions and/or insertions into the polypeptide sequence of less thanabout 50, less than about 40, less than about 30, less than about 20, orless than about 10 amino acid residues shall not be construed asaffecting homology. Homology or identity at the nucleotide or amino acidsequence level can be determined by BLAST (Basic Local Alignment SearchTool) analysis using the algorithm employed by the programs blastp,blastn, blastx, tblastn, and tblastx (Altschul (1997), Nucleic AcidsRes. 25, 3389-3402, and Karlin (1990), Proc. Natl. Acad. Sci. USA 87,2264-2268), which are tailored for sequence similarity searching. Theapproach used by the BLAST program is to first consider similarsegments, with and without gaps, between a query sequence and a databasesequence, then to evaluate the statistical significance of all matchesthat are identified, and finally to summarize only those matches whichsatisfy a preselected threshold of significance. For a discussion ofbasic issues in similarity searching of sequence databases, see Altschul(1994), Nature Genetics 6, 119-129. The search parameters for histogram,descriptions, alignments, expect (i.e., the statistical significancethreshold for reporting matches against database sequences), cutoff,matrix, and filter (low complexity) can be at the default settings. Thedefault scoring matrix used by blastp, blastx, tblastn, and tblastx isthe BLOSUM62 matrix (Henikoff (1992), Proc. Natl. Acad. Sci. USA 89,10915-10919), recommended for query sequences over 85 in length(nucleotide bases or amino acids).

For blastn, designed for comparing nucleotide sequences, the scoringmatrix can be set by the ratios of M (i.e., the reward score for a pairof matching residues) to N (i.e., the penalty score for mismatchingresidues), wherein the default values for M and N can be +5 and −4,respectively. Four blastn parameters can be adjusted as follows: Q=10(gap creation penalty); R=10 (gap extension penalty); wink=1 (generatesword hits at every winkth position along the query); and gapw=16 (setsthe window width within which gapped alignments are generated). Theequivalent Blastp parameter settings for comparison of amino acidsequences can be: Q=9; R=2; wink=1; and gapw=32. A Bestfit comparisonbetween sequences, available in the GCG package version 10.0, can useDNA parameters GAP=50 (gap creation penalty) and LEN=3 (gap extensionpenalty), and the equivalent settings in protein comparisons can beGAP=8 and LEN=2. The preceding parameter settings are exemplary only andother parameter settings may be used.

Thus, when referring to the polypeptide or nucleic acid sequences of thepresent invention, included are sequence identities of at least 40%, atleast 45%, at least 50%, at least 55%, of at least 70%, at least 65%, atleast 70%, at least 75%, at least 80%, or at least 85%, for example atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or about 100%sequence identity with the full-length polypeptide or nucleic acidsequence, or to fragments thereof comprising a consecutive sequence ofat least 50, at least 75, at least 100, at least 125, at least 150, atleast 200, or more than 200 amino acid residues of the entire protein;variants of such sequences, e.g., wherein at least one amino acidresidue has been inserted N- and/or C-terminal to, and/or within, thedisclosed sequence(s) which contain(s) the insertion and substitution.Contemplated variants can additionally or alternately include thosecontaining predetermined mutations by, e.g., homologous recombination orsite-directed or PCR mutagenesis, and the corresponding polypeptides ornucleic acids of other species, including, but not limited to, thosedescribed herein, the alleles or other naturally occurring variants ofthe family of polypeptides or nucleic acids which contain an insertionand substitution; and/or derivatives wherein the polypeptide has beencovalently modified by substitution, chemical, enzymatic, or otherappropriate means with a moiety other than a naturally occurring aminoacid which contains the insertion and substitution (for example, adetectable moiety such as an enzyme).

As used herein, the phrase “conservative amino acid substitution” or“conservative mutation” refers to the replacement of one amino acid byanother amino acid with a common property. A functional way to definecommon properties between individual amino acids is to analyze thenormalized frequencies of amino acid changes between correspondingproteins of homologous organisms (Schulz (1979) Principles of ProteinStructure, Springer-Verlag). According to such analyses, groups of aminoacids can be defined where amino acids within a group exchangepreferentially with each other, and therefore resemble each other mostin their impact on the overall protein structure (Schulz (1979)Principles of Protein Structure, Springer-Verlag). Examples of aminoacid groups defined in this manner can include: a “charged/polar group”including Glu, Asp, Asn, Gln, Lys, Arg, and His; an “aromatic or cyclicgroup” including Pro, Phe, Tyr, and Trp; and an “aliphatic group”including Gly, Ala, Val, Leu, Ile, Met, Ser, Thr, and Cys. Within eachgroup, subgroups can also be identified. For example, the group ofcharged/polar amino acids can be sub-divided into sub-groups including:the “positively-charged sub-group” comprising Lys, Arg and His; the“negatively-charged sub-group” comprising Glu and Asp; and the “polarsub-group” comprising Asn and Gln. In another example, the aromatic orcyclic group can be sub-divided into sub-groups including: the “nitrogenring sub-group” comprising Pro, His, and Trp; and the “phenyl sub-group”comprising Phe and Tyr. In another further example, the aliphatic groupcan be sub-divided into sub-groups including: the “large aliphaticnon-polar sub-group” comprising Val, Leu, and Ile; the “aliphaticslightly-polar sub-group” comprising Met, Ser, Thr, and Cys; and the“small-residue sub-group” comprising Gly and Ala. Examples ofconservative mutations include amino acid substitutions of amino acidswithin the sub-groups above, such as, but not limited to: Lys for Arg orvice versa, such that a positive charge can be maintained; Glu for Aspor vice versa, such that a negative charge can be maintained; Ser forThr or vice versa, such that a free —OH can be maintained; and Gln forAsn or vice versa, such that a free —NH2 can be maintained. A“conservative variant” is a polypeptide that includes one or more aminoacids that have been substituted to replace one or more amino acids ofthe reference polypeptide (for example, a polypeptide whose sequence isdisclosed in a publication or sequence database, or whose sequence hasbeen determined by nucleic acid sequencing) with an amino acid havingcommon properties, e.g., belonging to the same amino acid group orsub-group as delineated above.

As used herein, “expression” includes the expression of a gene at leastat the level of RNA production, and an “expression product” includes theresultant product, e.g., a polypeptide or functional RNA (e.g., aribosomal RNA, a tRNA, a guide RNA, an antisense RNA, a micro RNA, anshRNA, a ribozyme, etc.), of an expressed gene. The term “increasedexpression” includes an alteration in gene expression to facilitateincreased mRNA production and/or increased polypeptide expression.“Increased production” [of a gene product] includes an increase in theamount of polypeptide expression, in the level of the enzymatic activityof a polypeptide, or a combination of both, as compared to the nativeproduction or enzymatic activity of the polypeptide.

Some aspects of the present invention include the partial, substantial,or complete deletion, silencing, inactivation, or down-regulation ofexpression of particular polynucleotide sequences. The genes may bepartially, substantially, or completely deleted, silenced, inactivated,or their expression may be down-regulated in order to affect theactivity performed by the polypeptide they encode, such as the activityof an enzyme. Genes can be partially, substantially, or completelydeleted, silenced, inactivated, or down-regulated by insertion ofnucleic acid sequences that disrupt the function and/or expression ofthe gene (e.g., viral insertion, transposon mutagenesis, meganucleaseengineering, homologous recombination, or other methods known in theart). The terms “eliminate,” “elimination,” and “knockout” can be usedinterchangeably with the terms “deletion,” “partial deletion,”“substantial deletion,” or “complete deletion” and refer tosubstantially eliminating expression of the gene, for example, reducingthe level of expression to less than 10%, less than 5%, less than 2%, orless than 1% of control levels or undetectable levels. The terms“attenuation” and “knockdown” can be used to describe mutations andmanipulations resulting in a lower level of expression of a gene withrespect to wild type levels of expression, or, in some cases, resultingin reduced activity of a gene product, such as by mutating a functionaldomain of the encoded polypeptide. Attenuation can be completeattenuation (e.g., “knockout”) or can be partial attenuation, where, forexample, RNA or protein levels are reduced or “knocked down” by from1-99.5% of control levels, e.g., to a level where RNA or proteinexpression is detectable but reduced with respect to controls. Incertain embodiments, a microorganism of interest may be engineered bysite directed homologous recombination to knockout a particular gene ofinterest. In still other embodiments, RNAi or antisense DNA (asDNA)constructs may be used to partially, substantially, or completelysilence, inactivate, or down-regulate a particular gene of interest.

These insertions, deletions, or other modifications of certain nucleicacid molecules or particular polynucleotide sequences may be understoodto encompass “genetic modification(s)” or “transformation(s)” such thatthe resulting strains of the microorganisms or host cells may beunderstood to be “genetically modified”, “genetically engineered” or“transformed.”

As used herein, “up-regulated” or “up-regulation” includes an increasein expression of a gene or nucleic acid molecule of interest or theactivity of an enzyme, e.g., an increase in gene expression or enzymaticactivity as compared to the expression or activity in an otherwiseidentical gene or enzyme that has not been up-regulated.

As used herein, “down-regulated” or “down-regulation” includes adecrease in expression of a gene or nucleic acid molecule of interest orthe activity of an enzyme, e.g., a decrease in gene expression orenzymatic activity as compared to the expression or activity in anotherwise identical gene or enzyme that has not been down-regulated.

As used herein, “mutant” refers to an organism that has a mutation in agene that is the result of classical mutagenesis, for example, usinggamma irradiation, UV, or chemical mutagens. “Mutant” as used hereinalso refers to a recombinant cell that has altered structure orexpression of a gene as a result of genetic engineering that manyinclude, as non-limiting examples, overexpression, including expressionof a gene under different temporal, biological, or environmentalregulation and/or to a different degree than occurs naturally and/orexpression of a gene that is not naturally expressed in the recombinantcell; homologous recombination, including knock-outs and knock-ins (forexample, gene replacement with genes encoding polypeptides havinggreater or lesser activity than the wild type polypeptide, and/ordominant negative polypeptides); gene attenuation via RNAi, antisenseRNA, or ribozymes, or the like; and genome engineering usingmeganucleases, TALENs, and/or CRISPR technologies, and the like. Amutant is therefore not a naturally-occurring organism. A mutantorganism of interest will typically have a phenotype different than thatof the corresponding wild type or progenitor strain that lacks themutation, where the phenotype can be assessed by growth assays, productanalysis, photosynthetic properties, biochemical assays, etc. Whenreferring to a gene “mutant” means the gene has at least one base(nucleotide) change, deletion, or insertion with respect to a native orwild type gene. The mutation (change, deletion, and/or insertion of oneor more nucleotides) can be in the coding region of the gene or can bein an intron, 3′ UTR, 5′ UTR, or promoter region, e.g., within 2 kb ofthe transcriptional start site or within 3 kb or the translational startsite. As nonlimiting examples, a mutant gene can be a gene that has aninsertion within the promoter region that can either increase ordecrease expression of the gene; can be a gene that has a deletion,resulting in production of a nonfunctional protein, truncated protein,dominant negative protein, or no protein; can be a gene that has one ormore point mutations leading to a change in the amino acid of theencoded protein or results in aberrant splicing of the gene transcript,etc.

The term “Pfam” refers to a large collection of protein domains andprotein families maintained by the Pfam Consortium and available atseveral sponsored world wide web sites, including: pfam.xfam.org/(European Bioinformatics Institute (EMBL-EBI). The latest release ofPfam is Pfam 30.0 (June 2016). Pfam domains and families are identifiedusing multiple sequence alignments and hidden Markov models (HMMs).Pfam-A family or domain assignments, are high quality assignmentsgenerated by a curated seed alignment using representative members of aprotein family and profile hidden Markov models based on the seedalignment. (Unless otherwise specified, matches of a queried protein toa Pfam domain or family are Pfam-A matches.) All identified sequencesbelonging to the family are then used to automatically generate a fullalignment for the family (Sonnhammer (1998) Nucleic Acids Research 26,320-322; Bateman (2000) Nucleic Acids Research 26, 263-266; Bateman(2004) Nucleic Acids Research 32, Database Issue, D138-D141; Finn (2006)Nucleic Acids Research Database Issue 34, D247-251; Finn (2010) NucleicAcids Research Database Issue 38, D211-222). By accessing the Pfamdatabase, for example, using the above-referenced website, proteinsequences can be queried against the HMMs using HMMER homology searchsoftware (e.g., HMMER2, HMMER3, or a higher version, hmmer.org).Significant matches that identify a queried protein as being in a pfamfamily (or as having a particular Pfam domain) are those in which thebit score is greater than or equal to the gathering threshold for thePfam domain. Expectation values (e values) can also be used as acriterion for inclusion of a queried protein in a Pfam or fordetermining whether a queried protein has a particular Pfam domain,where low e values (much less than 1.0, for example less than 0.1, orless than or equal to 0.01) represent low probabilities that a match isdue to chance.

A “cDNA” is a DNA molecule that comprises at least a portion thenucleotide sequence of an mRNA molecule, with the exception that the DNAmolecule substitutes the nucleobase thymine, or T, in place of uridine,or U, occurring in the mRNA sequence. A cDNA can be double stranded orsingle stranded and can be, for example, the complement of the mRNAsequence. In preferred examples, a cDNA does not include one or moreintron sequences that occur in the naturally-occurring gene that thecDNA corresponds to (i.e., the gene as it occurs in the genome of anorganism). For example, a cDNA can have sequences from upstream of anintron of a naturally-occurring gene juxtaposed to sequences downstreamof the intron of the naturally-occurring gene, where the upstream anddownstream sequences are not juxtaposed in a DNA molecule in nature(i.e., the sequences are not juxtaposed in the naturally occurringgene). A cDNA can be produced by reverse transcription of mRNAmolecules, or can be synthesized, for example, by chemical synthesisand/or by using one or more restriction enzymes, one or more ligases,one or more polymerases (including, but not limited to, high temperaturetolerant polymerases that can be used in polymerase chain reactions(PCRs)), one or more recombinases, etc., based on knowledge of the cDNAsequence, where the knowledge of the cDNA sequence can optionally bebased on the identification of coding regions from genome sequences orcompiled from the sequences multiple partial cDNAs.

Reference to properties that are “substantially the same” or“substantially identical” without further explanation of the intendedmeaning, is intended to mean the properties are within 10%, andpreferably within 5%, and may be within 2.5%, within 1%, or within 0.5%of the reference value. Where the intended meaning of “substantially” ina particular context is not set forth, the term is used to include minorand irrelevant deviations that are not material to the characteristicsconsidered important in the context of the invention.

Although methods and materials similar or equivalent to those describedherein can be used in practice or testing of the present invention,suitable methods and materials are described below. The materials,methods, and examples are illustrative only and are not intended to belimiting. Other features and advantages of the invention will beapparent from the detailed description and from the claims.

A “control cell” or “control microorganism” is a cell or microorganismthat is substantially identical to the manipulated, recombinant, ormutant cell referred to, with the exception that the control cell doesnot have the modification of the manipulated, recombinant, or mutantcell. A control cell can be a wild type cell, for example a wild typecell of the strain from which the manipulated, recombinant, or mutantcell is directly or indirectly derived.

“The same conditions” or “the same culture conditions”, as used herein,means substantially the same conditions, that is, any differencesbetween the referenced conditions are minor and not relevant to thefunction or properties of the microorganism that are material to theinvention, e.g., lipid production or biomass production.

“Nitrogen replete” conditions, with respect to a particular cell type,are conditions under which the cell does not experience growthdeficiency due to insufficient nitrogen.

As used herein “lipid” or “lipids” refers to fats, waxes, fatty acids,fatty acid derivatives such as fatty alcohols, wax esters, alkanes, andalkenes, sterols, monoglycerides, diglycerides, triglycerides,phospholipids, sphingolipids, saccharolipids, and glycerolipids. “FAMElipids” or “FAME” refers to lipids having acyl moieties that can bederivatized to fatty acid methyl esters, such as, for example,monoacylglycerides, diacylglycerides, triacylglycerides, wax esters, andmembrane lipids such as phospholipids, galactolipids, etc. Lipidproductivity can be assessed as FAME productivity in milligrams perliter (mg/L) over a given time period (e.g., per day) and for algae, maybe reported as areal productivity, for example grams per meter² per day(g/m²/day). In the semi-continuous assays provided herein, mg/L/dayvalues are converted to g/m2/day by taking into account the area ofincident irradiance (the SCPA flask rack aperture of 1½″×3⅜″, or0.003145 m²) and the volume of the culture (550 ml). To obtainproductivity values in g/m2/day, mg/L/day values are multiplied by thedaily dilution rate (30%) and a conversion factor of 0.175. Where lipidor subcategories thereof (for example, TAG or FAME) are referred to as apercentage, the percentage is a weight percent unless indicatedotherwise.

“Biomass” refers to cellular mass, whether of living or dead cells, andcan be assessed, for example, as aspirated pellet weight, but is morepreferably dry weight (e.g., lyophilate of a culture sample or pelletedcells), ash-free dry weight (AFDW), or total organic carbon (TOC), usingmethods known in the art. Biomass increases during the growth of aculture under growth permissive conditions and may be referred to as“biomass accumulation” in batch cultures, for example. In continuous orsemi-continuous cultures that undergo steady or regular dilution,biomass that is produced that would otherwise accumulate in the cultureis removed during culture dilution. Thus, daily biomass productivity(increases in biomass) by these cultures can also be referred to as“biomass accumulation”. Biomass productivity can be assessed as TOCproductivity in milligrams per liter (mg/L) per given time period (e.g.,per day) and for algae, may be reported as grams per meter² per day(g/m²/day). In the semi-continuous assays provided herein, mg/L valuesare converted to g/m2/day by taking into account the area of incidentirradiance (the SCPA flask rack aperture of 1½″×3⅜″, or 0.003145 m²) andthe volume of the culture (550 ml). To obtain productivity values ing/m2/day, mg/L values are multiplied by the daily dilution rate (30%)and a conversion factor of 0.175. Where biomass is expressed as apercentage, the percentage is a weight percent unless indicatedotherwise.

In the context of the invention, a “nitrogen source” is a source ofnitrogen that can be taken up and metabolized by the subjectmicroorganism and incorporated into biomolecules for growth. Forexample, compounds including nitrogen that cannot be taken up and/ormetabolized by the microorganism for growth (e.g., nitrogen-containingbiological buffers such as Hepes, Tris, etc.) are not considerednitrogen sources in the context of the invention.

“Reduced nitrogen”, as used herein, is nitrogen in the chemical form ofammonium, ammonia, urea, or an amino acid that can be metabolized by themicroorganism being cultured to provide a source of nitrogen forincorporation into biomolecules, thereby supporting growth. For example,in addition to ammonium/ammonia and urea, reduced nitrogen can includevarious amino acids where the amino acid(s) can serve as a nitrogensource to the subject microorganism. Examples of amino acids caninclude, without limitation, glutamate, glutamine, histidine, lysine,arginine, asparagine, alanine, and glycine. “Non-reduced nitrogen” inthe context of a nitrogen source that can be present in a culture mediumfor microorganisms refers to nitrate or nitrite that must be reducedprior to assimilation into organic compounds by the microorganism.

“The sole source of nitrogen [in the culture medium]” is usedinterchangeably with “substantially the sole source of nitrogen” andindicates that no other nitrogen source is intentionally added to theculture medium and/or that no other nitrogen source is present in anamount sufficient to significantly increase the growth of themicroorganisms or cells cultured in the referenced medium. Throughoutthis application, for brevity, the terms “nitrate-only” and “urea-only”are used to characterize culture media in which nitrate is thesubstantially the sole source of nitrogen that is available to themicroorganisms for supporting growth or urea is the only source ofnitrogen that is available to the microorganisms for supporting growth,respectively.

Similarly, “the sole source of carbon [in the culture medium]” is usedinterchangeably with “substantially the sole source of carbon” andindicates that where inorganic carbon is substantially the sole sourceof carbon in the culture medium no other carbon source is present in anamount sufficient to increase the productivity or growth of themicroorganisms or cells cultured in the referenced medium or any othercarbon source that may be present is not significantly incorporated intobiomolecules such as lipids produced by the microorganisms or cells.“Inorganic carbon” refers to carbon dioxide, carbonate and carbonatesalts, and carbonic acid.

Disclosed herein are methods for manipulating, assaying, culturing, andanalyzing microorganisms. The invention set forth herein also makes useof standard methods, techniques, and reagents for cell culture,transformation of microorganisms, genetic engineering, and biochemicalanalysis that are known in the art.

All headings are for the convenience of the reader and do not limit theinvention in any way.

Mutant Microorganisms Having Increased Lipid Productivity

The invention provides mutant microorganisms having at least 45% of thebiomass productivity of a control microorganism and higher lipidproductivity (e.g., higher productivity per day, preferably averagedover the culture period) with respect to the control microorganism whenboth the mutant microorganism and control microorganism are culturedunder identical conditions in which the control microorganism culture isproducing biomass. Biomass productivity can be assessed, for example, asash-free dry weight (AFDW) production or productivity (i.e., amountproduced per day) or total organic carbon (TOC) productivity. A mutantmicroorganism as provided herein can demonstrate greater lipidproductivity than a control microorganism and at least 45% of thebiomass productivity of the control microorganism over a culture periodof at least three days, for example, a culture period of at least four,at least five, at least six, at least seven, at least eight, at leastnine, at least ten, at least eleven, at least twelve, at least thirteen,at least fourteen, at least fifteen, at least twenty, at least thirty,or at least sixty days when the mutant microorganism and the controlmicroorganism are cultured under conditions that support growth of thecontrol microorganism, i.e., under conditions in which the controlmicroorganism culture produces biomass. In some examples the cultureperiod in which a mutant microorganism as provided herein produces atleast 45% of the biomass and produces more lipid with respect to acontrol microorganism can be less than 180 days, less than 120 days, orless than 90 days. In some examples, a mutant microorganism as providedherein produces higher amounts of lipid with respect to a controlmicroorganism under culture conditions in which both the mutant andcontrol microorganism are producing biomass and the mutant produces atleast 45%, at least 50%, at least 55%, at least 60%, at least 65%, atleast 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 95%, at least 100%, at least 105%, at least 110%, or at least 120%of the biomass produced by a control microorganism on a daily basis. Insome examples, a mutant microorganism as provided herein produces higheramounts of lipid with respect to a control microorganism and at least45% of the biomass but less than 300% or less than 325%, or less than200% of the biomass produced by the control microorganism. In someexamples, a mutant microorganism as provided herein produces higheramounts of lipid with respect to a control microorganism under cultureconditions in which both the mutant and control microorganism areproducing biomass and actively dividing.

Methods of measuring the amount of lipid produced by microorganisms arewell-known in the art and provided in the examples herein. Totalextractable lipid can be determined according to Folch et al. (1957) J.Biol. Chem. 226: 497-509; Bligh & Dyer (1959) Can. J. Biochem. Physiol.37: 911-917; or Matyash et al. (2008) J. Lipid Res. 49:1137-1146, forexample, and the percentage of biomass present as lipid can also beassessed using Fourier transform infrared spectroscopy (FT-IR)(Pistorius et al. (2008) Biotechnol & Bioengin. 103:123-129). Additionalreferences for gravimetric analysis of FAME and TAGS are provided inU.S. Pat. No. 8,207,363 and WO 2011127118 for example, each incorporatedherein by reference in its entirety. FAME analysis methods can also befound for example as American Oil Chemists' Society Methods Ce 1b-89 andCe 1-62 (aocs.org/Methods/).

Biomass can be assessed by measuring total organic carbon (TOC) or byother methods, such as measuring ash-free dry weight (AFDW). Methods formeasuring TOC are known in the art (e.g., U.S. Pat. No. 8,835,149) andare provided herein. Methods of measuring AFDW are also well-known andcan be found, for example, in U.S. Pat. No. 8,940,508, incorporatedherein by reference in its entirety.

A mutant microorganism can produce, for example, at least 25% more lipidthan a control microorganism and at least 45% as much biomass as thecontrol microorganism during a culture period of at least three, four,five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen,fifteen, twenty, thirty, or sixty days during which both the mutant andcontrol microorganisms produce biomass. For example, the average dailylipid productivity can be at least 25% greater than the average dailylipid productivity of a control microorganism and the average dailybiomass productivity can be at least 45% as much as the biomassproductivity of the control microorganism during a culture period of atleast three, four, five, six, seven, eight, nine, ten, eleven, twelve,thirteen, fourteen, fifteen, twenty, thirty, or sixty days. Inadditional examples, a mutant microorganism can produce at least about50% more lipid than is produced by a control microorganism and at least45% as much biomass as the control microorganism, i.e., can exhibit nomore than a 55% reduction in biomass with respect to the controlmicroorganism, under conditions in which the control microorganism isproducing biomass. A mutant can in some examples produce less than 400%or less than 300% more lipid than a control microorganism whileaccumulating at least 45% as much biomass as the control microorganismduring a culture period of at least three, four, five, six, seven,eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, twenty,thirty, or sixty days.

The culture conditions under which a mutant as provided herein producesat least 25% or at least about 50% more FAME while producing at least50% of the amount of TOC as a control microorganism can be nutrientreplete, and can be nitrogen replete with respect to the controlmicroorganism, that is, the culture conditions can be sufficient innutrients with respect to the control microorganism such that additionalnutrients do not increase the growth rate of the microorganism (whereall other culture conditions and ingredients remain the same). Forexample, the culture conditions can be sufficient in nitrogen withrespect to the control microorganism such that additional nitrogen donot increase the growth rate of the microorganism (where all otherculture conditions and ingredients remain the same). Alternatively, insome embodiments the culture conditions under which a mutant as providedherein produces at least 25% or at least 50% more FAME (which can be theaverage daily FAME productivity) while producing at least 45% of theamount of TOC (e.g., the average daily TOC productivity) as a controlmicroorganism can include nitrogen that supports biomass production, butat a lower rate than fully nitrogen replete culture media. For example,the culture conditions may allow for biomass (TOC or AFDW) production atleast 60%, at least 65%, at least 70%, at least 75%, at least 80%, atleast 85%, at least 90%, or at least 95% the rate of biomass productionin fully nitrogen replete culture media.

Mutant microorganisms disclosed herein can produce at least 25% morelipid, e.g., 25% more FAME, as is produced by a control microorganism,while producing at least 45% of the biomass of the control microorganismunder conditions that support biomass production that is comparable tothe levels of biomass of the control microorganism undernitrogen-replete conditions. For example, biomass production of thecontrol microorganism can be within 20% or within 15% of the biomassproduction of the control microorganism under nitrogen-repleteconditions. Alternatively or in addition, a mutant as provided hereincan produce at least 45% of the biomass of the control microorganismwhile producing at least 25% more lipid than the control microorganism,where the mutant and control microorganism are cultured under conditionsthat are nitrogen replete with respect to the control microorganism. Invarious examples, the mutant can produce at least 45% of the biomassproduced by a control cell and at least 25% more lipid than the controlcell over the same time period in a culture that includes one or more ofnitrate or urea, and in some examples can further optionally includeless than about 5 mM ammonium, such as less than about 2.5 mM, ammonium,less than about 2 mM ammonium, less than about 1.5 mM ammonium,ammonium, less than about 1 mM ammonium, about 0.5 mM ammonium, or lessthan 0.5 mM ammonium.

In particular nonlimiting examples, a microorganism can be an algal orheterokont microorganism and can produce at least 25% more FAME whileproducing at least 45% of the amount of TOC as is produced by a controlalgal or heterokont microorganism in a culture medium that includes lessthan about 5 mM, less than about 4.5 mM, less than about 4 mM, less thanabout 3.5 mM, less than about 3 mM, less than about 2.5 mM, less thanabout 1 mM, or less than about 0.5 mM ammonium. For example, theammonium concentration may be at a concentration ranging from about 0 toabout 5 mM, from about 0 to about 4.0 mM, from about 0 to about 3 mM,from about 0 to about 2.5 mM, from about 0 to about 2.0 mM, from about 0to about 1.5 mM, from about 0 to about 1.0 mM, or from about 0 to about0.5 mM. The ammonium concentration may be at a concentration rangingfrom about from about 0.5 to about 5 mM, from about 0.5 to about 4 mM,from about 0.5 to about 3 mM, 0.5 to about 2.5 mM, from about 0.5 toabout 2.0 mM, from about 0.5 to about 1.5 mM, about 0.5 to about 1 mM,or from about 1 to about 5 mM, about 1 to about 2.5 mM, or from about0.1 to about 1 mM, from about 0.1 to about 1.5 mM, or from about 0.1 toabout 2 mM. In further examples, the ammonium concentration may be at aconcentration ranging from about 1 mM to about 2.5 mM or from about 0.2to about 1.5 mM.

In some examples, a mutant microorganism can be an algal or heterokontcell that produces at least 25% more FAME while producing at least 45%of the amount of TOC as a control microorganism in a culture medium thatincludes about 2.5 mM ammonium or less, about 2.0 mM ammonium or less,about 1.5 mM ammonium or less, about 1.0 mM ammonium or less, about 0.5mM ammonium or less, or substantially no ammonium, and can optionallyinclude, for example, at least 1.0 mM, at least 2.0 mM, at least 3.0 mM,at least 4.0 mM, at least 5.0 mM, at least 6.0 mM, at least 7.0 mM, atleast 8.0 mM, or at least 10.0 mM nitrate and/or urea. In furthernonlimiting examples, a microorganism can be an algal or heterokont celland can produce at least 50% more FAME while producing at least 45% ofthe amount of TOC as a control microorganism on a culture medium thatincludes less than about 5 mM, less than about 2.5 mM, less than about 1mM, or less than about 0.5 mM ammonium. For example, a microorganism canbe an algal or heterokont cell that produces at least 50% more FAMEwhile producing at least 45% of the amount of TOC as a controlmicroorganism in a culture medium that includes about 2.5 mM ammonium orless, about 1.0 mM ammonium or less, about 0.5 mM ammonium or less, orsubstantially no ammonium, and can include, for example, at least 1.0mM, at least 2.0 mM, at least 3.0 mM, at least 4.0 mM, at least 5.0 mM,at least 6.0 mM, at least 7.0 mM, at least 8.0 mM, or at least 10.0 mMnitrate and/or urea.

The mutant microorganisms provided herein can have greater partitioningof carbon to lipid with respect to a control microorganism culturedunder identical conditions in which both the control microorganism andthe mutant microorganism are producing biomass. A mutant havingincreased partitioning of carbon to lipid with respect to a controlmicroorganism can have increased partitioning of carbon to totalextractable lipid, to total neutral lipids, to triglycerides, and/or toFAME-derivatizable lipids. For example, a mutant microorganism asprovided herein can have a ratio of the amount of FAME-derivatizablelipids (“FAME”) produced to biomass (TOC or ash-free dry weight (AFDW),for example) produced that is at least 50% higher than that of a controlmicroorganism. Lipid and biomass production and/or production can beassessed, for example, by gravimetric analysis as known in the art anddemonstrated in the examples herein. For example, a mutant microorganismas provided herein can have a ratio of FAME to TOC that is at least 50%,at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, atleast 80%, at least 85, at least 90%, at least 95%, at least 100%, atleast 110%, at least 120%, at least 130%, at least 140%, at least 150%,at least 160%, at least 170%, at least 180%, at least 190%, at least200%, or at least 250% higher than the FAME/TOC ratio of a controlmicroorganism when both the mutant microorganism and the controlmicroorganism are cultured under conditions in which both the culture ofthe mutant microorganism and the culture of the control microorganismproduce biomass. In some example, the FAME/TOC ratio of a mutantmicroorganism as provided herein can be increased with respect to theFAME/TOC ratio of a control microorganism cultured under identicalconditions by less than about 300%.

In various examples a mutant microorganism as provided herein can have aratio of the amount of FAME produced to TOC produced that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85, at least 90%, at least 95%, at least100%, at least 110%, at least 120%, at least 130%, at least 140%, atleast 150%, at least 160%, at least 170%, at least 180%, at least 190%,at least 200%, or at least 250% higher than the FAME/TOC ratio of acontrol microorganism when both the mutant microorganism and the controlmicroorganism are cultured under conditions in which the control cultureproduces biomass (e.g., TOC) and the mutant culture produces at least45%, at least 50%, at least 60%, at least 70%, at least 80%, at least90%, or at least 95% of the amount of biomass that is produced by thecontrol culture. In various examples, the FAME/TOC ratio of a mutant asprovided herein can be at least 0.30, at least 0.35, at least 0.40, atleast 0.45, at least 0.50, at least 0.55, at least 0.60, at least 0.65,at least 0.7, or at least 0.75 when cultured under conditions in whichthe mutant microorganism culture produces at least 45%, at least 50%, atleast 60%, at least 65%, at least 70%, at least 75%, at least 80%, atleast 85, at least 90%, or at least 95% as much biomass (e.g., TOC) as acontrol microorganism culture, under conditions where both the controland mutant cultures produce biomass. In various examples, the FAME/TOCratio of a mutant as provided herein can be at least 0.30, at least0.35, at least 0.40, at least 0.45, at least 0.50, at least 0.55, atleast 0.60, at least 0.65, at least 0.7, or at least 0.75 when culturedunder conditions in which the mutant culture produces at least about50%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85, at least 90%, at least 95%, or at least 100% as muchbiomass (e.g., TOC) as a control microorganism produces when culturedunder nitrogen replete conditions.

In some examples, a mutant microorganism as provided herein can produceat least 50% more FAME while producing at least 80%, at least 85%, or atleast 90% of the TOC produced by a control cell (such as a wild typecell) when cultured under conditions in which both the control andmutant microorganism produce biomass, and the FAME/TOC ratio of themutant microorganism is at least 40%, at least 50%, at least 60%, atleast 70%, or at least 75% higher than the FAME/TOC of the controlmicroorganism. The FAME/TOC ratio of the mutant microorganism can be,for example, at least 0.30, at least 0.35, or at least 0.40. The cultureconditions can include, for example, a culture medium that includes lessthan 5 mM, less than 2.5 mM, less than 2 mM, less than 1.5 mM, less than1.0 mM, or less than 0.5 mM ammonium and can include at least 2 mM, atleast 4 mM, or at least 6 mM urea or nitrate. In additional examples amutant microorganism as provided herein can produce at least 60%, atleast 70%, or at least 80% more FAME while producing at least 85%, atleast 90%, or at least 95% of the TOC produced by a control cell (suchas a wild type cell) when cultured under conditions in which both wildtype and mutant microorganism are producing biomass, and the FAME/TOCratio of the mutant microorganism is at least 50%, at least 60%, atleast 70%, or at least 75% greater than the FAME/TOC ratio of thecontrol microorganism. The FAME/TOC ratio of the mutant microorganismcan be, for example, at least 0.35, at least 0.40, or at least 0.45. Theculture conditions can include, for example, a culture medium thatincludes less than 2.5 mM, less than 1.0 mM, or less than 0.5 mMammonium and can include at least 2 mM, at least 4 mM, or at least 6 mMurea or nitrate. The culture conditions can in some examples includesubstantially no ammonium, and in some examples can includesubstantially no reduced nitrogen as a nitrogen source.

In yet further examples a mutant microorganism as provided herein canproduce at least 85%, at least 90%, at least 95%, at least 100%, atleast 105%, at least 110%, or at least 115% more FAME while producing atleast 70%, at least 75%, at least 80%, or at least 85% of the TOCproduced by a control cell (such as a wild type cell) when culturedunder conditions in which both wild type and mutant microorganism areproducing biomass, and the FAME/TOC ratio of the mutant microorganism isat least 100%, at least 110%, at least 120%, at least 130%, at least140%, at least 150%, at least 160%, at least 170%, or at least 180%greater than the FAME/TOC ratio of the control microorganism. FAME andTOC production can be assessed as average daily FAME productivity overthe culture period, for example over a culture period of at least three,at least five, at least ten, at least twenty, at least thirty, or atleast sixty days, or a culture period of between three and sixty days,or between three and thirty days, for example between three and fifteendays or between five and fifteen days. The FAME/TOC ratio of the mutantmicroorganism can be, for example, at least 0.50, at least 0.55, atleast 0.60, at least 0.65, at least 0.70, or at least 0.75. The cultureconditions can include, for example, a culture medium that includes lessthan 2.5 mM, less than 1.0 mM, or less than 0.5 mM ammonium and caninclude at least 2 mM, at least 4 mM, or at least 6 mM urea or nitrate.

In additional examples, a mutant microorganism can produce at leastabout 70% of the biomass produced by a wild type or controlmicroorganism and at least 90% more lipid than is produced by a wildtype or control microorganism when the mutant microorganism and wildtype or control microorganism are cultured under the same conditions.FAME and TOC production can be assessed as average daily FAMEproductivity over the culture period, for example over a culture periodof at least three, at least five, at least ten, at least twenty, atleast thirty, or at least sixty days. For example the wild type andcontrol microorganism can be cultured in batch, semi-continuous, orcontinuous culture for at least three, four, five, six, seven, eight,nine, ten, eleven, twelve, thirteen, fourteen, fifteen, twenty, thirty,or sixty days. In some examples the concentration of ammonium in theculture medium may be less than about 5 mM or less than about 2.5 mM. Insome examples the culture medium may include at least 2 mM nitrate or atleast 2 mM urea. The mutant microorganism can produce, in some examples,at least about 75% or at least about 80% of the biomass produced by awild type or control microorganism and at least 100% or at least 110%more lipid than is produced by a wild type or control microorganism whenthe mutant microorganism and wild type or control microorganism arecultured under the same conditions. The FAME/TOC ratio can be at least80%, at least 100%, at least 120%, or at least 150% greater than theFAME/TOC ratio of a wild type microorganism cultured under the sameconditions. In some examples, the mutant microorganism can produce atleast about 70% or at least about 75% of the biomass produced by a wildtype or control microorganism and at least 100% or at least 120% moreFAME lipids than are produced by a wild type or control microorganismwhen the mutant microorganism and wild type or control microorganism arecultured under the same conditions, and the mutant microorganism canhave a FAME/TOC ratio at least 100% or at least 120% greater than theFAME/TOC ratio of a wild type microorganism cultured under the sameconditions.

In various embodiments, a mutant microorganism as provided herein, e.g.,a mutant microorganism such as any described herein that produces atleast about 50% of the biomass and at least about 50%, at least 55%, atleast 60%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 95%, at least 100%, at least 110%, at least 120%, atleast 125%, or at least 130% more lipid than is produced by a controlmicroorganism cultured under the same conditions, where the conditionssupport daily biomass accumulation by the control microorganism, canhave a higher carbon to nitrogen (C:N) ratio than a controlmicroorganism. For example, the C:N ratio can be from about 1.5 to about2.5 the C:N ratio of a control microorganism when the mutantmicroorganism and the control microorganism are cultured underconditions in which both the mutant and the control microorganismsaccumulate biomass, and the mutant produces at least 50%, at least 60%,at least 70%, at least 80%, at least 90% or at least 100% more lipidthat the control microorganism and at least 50%, at least 60%, at least70%, at least 80%, or at least 85% of the TOC of the controlmicroorganism. In some embodiments the C:N ratio of a mutant as providedherein is between about 7 and about 20 or between about 8 and about 17,or between about 10 and about 15 during the culturing in which mutantproduces at least 50% more lipid that a control microorganism whileproducing at least 50% as much biomass as the control microorganism. Acontrol microorganism in any of the embodiments or examples herein canbe a wild type microorganism.

Alternatively or in addition, mutant microorganism as provided herein,e.g., a mutant microorganism such as any described herein that producesat least about 50% of the biomass and at least about 50%, at least 55%,at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 95%, at least 100%, at least 110%, or at least 120%more lipid than is produced by a control microorganism cultured underthe same conditions, where the conditions support daily biomassaccumulation by the control microorganism, can have reduced proteincontent when compared with a control microorganism. For example, in someembodiments a mutant microorganism as provided herein can have adecrease in protein content of at least 10%, at least 20%, at least 30%,at least 40%, at least 45%, or at least 50% with respect to a controlmicroorganism.

In various embodiments, a mutant microorganism as provided herein canhave attenuated expression of a gene encoding a protein whose expressionaffects the expression of other genes, e.g., at least ten, at leasttwenty, at least thirty, at least forty, at least fifty, at least sixty,at least seventy, at least eighty, at least ninety, or at least 100additional genes. For example, a mutant as provided herein can have atleast ten genes that are upregulated with respect to a wild typemicroorganism and at least ten genes that are downregulated with respectto a wild type microorganism under conditions in which the mutantphenotype (greater lipid production) is expressed. A mutant as providedherein can have at least twenty, at least thirty, at least forty, atleast fifty, at least sixty, at least seventy, at least eighty, at leastninety, or at least 100 genes that are upregulated with respect to awild type microorganism and at least twenty, at least thirty, at leastforty, at least fifty, at least sixty, at least seventy, at leasteighty, at least ninety, or at least 100 genes that are downregulatedwith respect to a wild type microorganism under conditions in which themutant phenotype (e.g., greater lipid production with respect to thewild type microorganism) is expressed. In some embodiments, genesencoding polypeptides involved in protein synthesis can be upregulatedin a mutant as provided herein, for example, genes encoding ribosomalpolypeptides or other polypeptides that function in translation,including, without limitation, those belonging to gene ontology (GO)groups such as “translation”, “ribosome”, “structural constituent ofribosome”, “eukaryotic translation initiation factor 3 complex”,“translation initiation factor activity”, “translational initiation”,“small ribosomal subunit”, “formation of translation preinitiationcomplex”, regulation of translation initiation, “eukaryotic 43Spreinitiation complex”, and “eukaryotic 48S preinitiation complex”.Alternatively or in combination with the upregulation of genes encodingpolypeptides relating to protein synthesis, any of various genesencoding polypeptides involved in nitrogen assimilation such as amolybdenum cofactor biosynthesis protein, a nitrate transporter, anitrate reductase, a nitrite reductase, a glutamate synthase, aglutamine synthase, a glutamate dehydrogenase, and an ammoniumtransporter can be downregulated in a mutant as provided herein.Alternatively or in combination with any of the above, a mutant asprovided herein can exhibit upregulation of certain genes related tolipid biosynthesis including but not limited to a lipid droplet surfaceprotein and/or one or more desaturases, elongases, lipases,acyltransferases, and/or glyceraldehyde-3-phosphate dehydrogenases.

The properties of a mutant as provided herein having increased lipidproduction are compared to the same properties of a controlmicroorganism that may be a wild type organism of the same species asthe mutant, preferably the progenitor strain of the lipid-overproducingmutant. Alternatively, a control microorganism can be a microorganismthat is substantially identical to the mutant microorganism with theexception that the control microorganism does not have the mutation thatleads to higher lipid productivity. For example, a control microorganismcan be a genetically engineered microorganism or classically mutatedorganism that has been further mutated or engineered to generate amutant having increased lipid productivity and/or increased lipidpartitioning as disclosed herein.

In some examples, a control microorganism can be a microorganism that issubstantially identical to the mutant microorganism, with the exceptionthat the control microorganism does not have a mutation in a gene orattenuated expression of a gene that regulates lipid induction (i.e.,the gene whose mutation results in increased lipid production underconditions in which the mutant microorganism has at least about half thebiomass productivity of the progenitor strain). The properties of alipid-overproducing mutant having a disrupted, attenuated, or otherwisedirectly or indirectly genetically manipulated gene (resulting inaltered structure or expression of the lipid induction regulator gene)are also be compared with the same properties of a control cell thatdoes not have a disrupted, attenuated, or otherwise directly orindirectly genetically manipulated lipid induction regulator generesulting in altered structure or expression of the lipid inductionregulator gene (regardless of whether the cell is “wild-type”). Forexample, a control cell may be a recombinant cell or a cell mutated in agene other than the lipid induction regulator gene whose effects arebeing assessed, etc.

Heterokont species considered for use in the invention include, but arenot limited to, Bacillariophytes, Eustigmatophytes, Labrinthulids, andThraustochytrids, such as, for example, species of Labryinthula,Labryinthuloides, Thraustochytrium, Schizochytrium, Aplanochytrium,Aurantiochytrium, Oblongichytrium, Japonochytrium, Diplophrys, orUlkenia.

Mutant microorganisms having the properties disclosed herein, such asmutant microorganisms having attenuated expression of a gene thatregulates lipid biosynthesis, such as the ZnCys-2845 gene of N. gaditanaand orthologs thereof can be, in various examples, of any eukaryoticmicroalgal strain such as, for example, any species of any of the generaAchnanthes, Amphiprora, Amphora, Ankistrodesmus, Asteromonas,Boekelovia, Bolidomonas, Borodinella, Botrydium, Botryococcus,Bracteococcus, Chaetoceros, Carteria, Chlamydomonas, Chlorococcum,Chlorogonium, Chlorella, Chroomonas, Chrysosphaera, Cricosphaera,Crypthecodinium, Cryptomonas, Cyclotella, Desmodesmus, Dunaliella,Elipsoidon, Emiliania, Eremosphaera, Ernodesmius, Euglena, Eustigmatos,Franceia, Fragilaria, Fragilaropsis, Gloeothamnion, Haematococcus,Hantzschia, Heterosigma, Hymenomonas, Isochrysis, Lepocinclis,Micractinium, Monodus, Monoraphidium, Nannochloris, Nannochloropsis,Navicula, Neochloris, Nephrochloris, Nephroselmis, Nitzschia,Ochromonas, Oedogonium, Oocystis, Ostreococcus, Parachlorella,Parietochloris, Pascheria, Pavlova, Pelagomonas, Phceodactylum, Phagus,Picochlorum, Platymonas, Pleurochrysis, Pleurococcus, Prototheca,Pseudochlorella, Pseudoneochloris, Pseudostaurastrum, Pyramimonas,Pyrobotrys, Scenedesmus, Schizochlamydella, Skeletonema, Spyrogyra,Stichococcus, Tetrachlorella, Tetraselmis, Thalassiosira, Tribonema,Vaucheria, Viridiella, Vischeria, and Volvox. Non-limiting examples ofparticularly suitable species include, for instance, heterokont algae,such as but not limited to diatoms such as, for example, a species ofany of the genera Amphora, Chaetoceros, Cyclotella, Fragilaria,Fragilaropsis, Hantzschia, Navicula, Nitzschia, Phceodactylum, orThalassiosira, or Eustigmatophytes, e.g., Chloridella, Chlorobptrys,Ellipsoidion, Eustigmatos, Goniochloris, Monodopsis, Monodus,Nannochloropsis, Pseudocharaciopsis, Pseudostaruastrum,Pseudotetraëdriella, or Vischeria. In some examples, the mutant algacell is a species of Ellipsoidion, Eustigmatos, Monodus,Nannochloropsis, Pseudostaruastrum, Pseudotetraëdriella, or Vischeria.In some examples, the mutant alga cell is a species of Nannochloropsis,e.g., N. gaditana, N. granulata, N. limnetica N. oceanica, N oculata, orN sauna.

The mutants can be spontaneous mutants, classically-derived mutants, orengineered mutants having attenuated expression of a regulator gene. Forexample, a mutant microorganism such as any described herein can be amutant obtained by classical mutagenesis or genetic engineering. Inparticular embodiments, a mutant microorganism as provided herein is agenetically engineered mutant, for example, a microorganism into whichat least one exogenous nucleic acid molecule has been introduced, e.g.,into which at least one recombinant nucleic acid molecule has beenintroduced, where the mutant microorganism is genetically engineered toinclude the exogenous nucleic acid molecule and/or the exogenous nucleicacid molecule effects at least one alteration of the microorganism'sgenome.

In various examples, the mutant microorganism is an algal or heterokontspecies and has attenuated expression of a gene that encodes apolypeptide having at least 50%, at least 55%, at least 60%, at least65%, at least 70%, at least 75%, at least 80%, at least 85%, at least90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6,SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQID NO:17 and/or has a coding region having at least 50%, at least 55%,at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, atleast 85%, at least 90%, or at least 95% identity SEQ ID NO:1 or any ofSEQ ID NOs:72-84. Alternatively or in addition, the mutant microorganismis an algal or heterokont species and has attenuated expression of agene that encodes a polypeptide having an amino acid sequence with atleast 55%, at least 60%, at least 65%, at least 70%, at least 75%, atleast 80%, at least 85%, at least 90%, or at least 95% identity to aminoacids 1-200 of SEQ ID NO:20 or to SEQ ID NO:18 or SEQ ID NO:19. Themutant microorganism can in certain embodiments further include a domainhaving at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, or at least 95% identityto any of SEQ ID NOs:21-25. The domain can be a PAS3 domain. The mutantmicroorganism can be engineered to attenuate expression of at least onegene encoding a polypeptide as set forth herein by any gene attenuationmethod, such as any disclosed herein or equivalents thereof.

The polypeptide encoded by the gene whose expression is attenuated canbe a transcription factor protein of the Zn(II)2Cys6 fungal-typeDNA-binding domain protein family. The polypeptide encoded by the genewhose expression is attenuated can include a Zn(2)Cys(6) domain,categorized as conserved domain cd00067 by the NCBI conserved domaindatabase (ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml), referred to as the“GAL4-like Zn2Cys6 binuclear cluster DNA-binding domain” that is foundin transcription factors such as GAL4, also characterized as smart00066:“GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-bindingdomain”. This domain, which may be referred to herein as a Zn2Cys6,Zn₂Cys₆, or Zn(2)Cys(6) domain or simply a ZnCys domain, occurs at aminoacids 190-219 of SEQ ID NO:2, is also characterized as pfam PF00172(“Zn_Clus” or “Fungal Zn(2)-Cys(6) binuclear cluster domain”) with agathering cutoff for this family of 20.8. In some embodiments, a mutantas provided herein can have attenuated expression of a gene encoding apolypeptide having a Zn(2)Cys(6) domain having at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, or at least 95% identity to SEQ IDNO:3.

Alternatively or in addition, the gene whose expression is attenuatedcan encode a polypeptide having a PAS_3 domain (pfam 08447, having agathering cutoff of 25.6) also called “PAS fold domain” or simply a PASdomain, such as, for example, a PAS domain having at least at least 55%,at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, atleast 85%, at least 90%, or at least 95% identity to any of SEQ IDNOs:21-25.

The mutant microorganism having attenuated expression of a gene thatregulates lipid production can be a “knockout” mutant, for example, inwhich the reading frame of the polypeptide is disrupted such that afunctional protein is not produced. For example, the gene can include aninsertion, deletion, or mutation in the reading frame that results in nofunctional protein being made. The insertion, deletion, or mutation canbe made by various means, such as, for example, homologous recombinationconstructs, RNA-guided endonucleases that employ guide RNAs, optionallyin combination with donor DNA fragments, etc. In other examples, themutant microorganism can be a “knockdown” mutant in which expression ofthe gene is reduced with respect to a wild type cell. For example,transcript levels of the target gene, which may be, for example, a geneencoding a Zn(2)-C6 fungal-type DNA-binding domain protein, can bereduced between about 5% and about 95% or between about 10% and about90% with respect to the transcript level in a control microorganism,such as a wild type microorganism. Knockdowns can be mutants in which amutation, insertion, or deletion occurs in a non-coding region of thegene or can be effected by expressing constructs in the cells thatreduce expression of the targeted gene, such as ribozyme, RNAi, orantisense constructs. In some embodiments gene attenuation can beeffected by insertion of a DNA fragment into a noncoding region of thegene, such as a 5′UTR or 3′ UTR. Insertion of a DNA fragment canoptionally be by use of an RNA-guided endonuclease, e.g., a cas protein.The mutant microorganism having attenuated expression of a gene thatregulates lipid production can include, for example, one or more of anRNAi construct for expressing RNAi or one or more RNAi molecules, anantisense construct for expressing antisense RNA or one or moreantisense molecules, a ribozyme construct for expressing a ribozyme orone or more ribozymes, one or more guide RNAs, one or more constructsfor expressing a guide RNA, one or more donor fragments for cas-mediatedinsertion, one or more homologous recombination constructs, one or moregenes encoding a cas enzyme, or a cas enzyme, one or more genes encodinga TALEN, or one or more TALENs, or one or more meganucleases.

Thus, provided herein are microorganisms that have attenuated expressionof a gene encoding a polypeptide of the Zn(II)2Cys6 family, i.e., apolypeptide that includes a “GAL4-like Zn2Cys6 binuclear clusterDNA-binding domain” (NCBI conserved domain cd00067) and/or recruits topfam PF00172 (“Zn_Clus” or “Fungal Zn(2)-Cys(6) binuclear clusterdomain”) with a bit score greater than the gathering cutoff for thisfamily of 20.8. Alternatively or in addition a mutant microorganism asprovided herein may have attenuated expression of a gene encoding apolypeptide that includes a PAS domain (e.g., a “PAS3 domain” or “PASfold domain”) that may be characterized as PF08447 or PF00989. Themutant can produce more lipid that a control microorganism under cultureconditions in which both the mutant and the control microorganismproduce biomass and in which the mutant microorganism produces at least50% of the biomass as is produced by the control microorganism. Forexample, the mutant microorganism can produce at least 25%, at least30%, at least 35%, at least 40%, at least 45%, at least 50%, at least60%, at least 70%, at least 80%, at least 90%, at least 100%, at least110% or at least 120% more lipid that a control microorganism underculture conditions in which both the mutant and the controlmicroorganism produce biomass and in which the mutant microorganismproduces at least 50% of the biomass as is produced by the controlmicroorganism. In various embodiments the microorganism that hasattenuated expression of a gene encoding a polypeptide of theZn(II)2Cys6 family and/or having a PAS domain produces at least 50% morethe lipid and at least 50% of the biomass as is produced by a controlmicroorganism on a daily basis for at least five, at least six, at leastseven, at least eight, at least nine, at least ten, at least eleven, orat least twelve-days of culturing. The mutant can include any of theproperties described hereinabove, including, without limitation,increased FAME/TOC ratio under conditions in which the mutant producesmore lipid that a control microorganism. The culture conditions underwhich the mutant produces a higher amount of lipid while producing atleast 50% of the biomass as control microorganism can include less than2.5 mM, less than 1.5 mM, less than 1 mM, or about 0.5 mM or lessammonium. The culture conditions under which the mutant produces ahigher amount of lipid while producing at least 50% of the biomass ascontrol microorganism can include a culture medium that includesnitrate, such as at least 2, 3, 4, or 5 mM nitrate. Alternatively or inaddition, the culture conditions can include a culture medium thatincludes urea, such as at least 2, 3, 4, or 5 mM urea. The culture insome examples can provide nitrate as substantially the sole source ofnitrogen available to the mutant and control microorganism. The controlmicroorganism can be a wild type microorganism of the same species asthe mutant, e.g., can be a wild type strain from which the mutant wasderived. The microorganism can be an alga or a heterokont, and in someexamples is a heterokont alga such as, but not limited to, a diatom oreustigmatophyte. In various examples lipid can be measured as FAMElipids, and biomass can be measured as, for example, TOC.

Alternatively or in addition, a mutant microorganism as provided hereinhaving attenuated expression of a gene encoding a polypeptide of theZn(II)2Cys6 family can demonstrate a FAME/TOC ratio that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85, at least 90%, at least 95%, at least100%, at least 110%, at least 120%, at least 130%, at least 140%, atleast 150%, at least 160%, at least 170%, at least 180%, at least 190%,at least 200%, or at least 250% higher than the FAME/TOC ratio of acontrol microorganism when both the mutant microorganism and the controlmicroorganism are cultured under conditions in which the control cultureproduces biomass (e.g., TOC) and the mutant culture produces at least45%, at least 50%, at least 60%, at least 70%, at least 80%, at least90%, or at least 95% of the amount of biomass that is produced by thecontrol culture. In an exemplary embodiment, a ZnCys attenuation straincan exhibit about twice the lipid productivity of a control strain(e.g., a wild type strain), while allocating approximately 35-70% of itscarbon to lipid, for example, while allocating from about 40% to about65% of its carbon to lipid, such as about 45%, 50%, 60%, or 65% of itscarbon to lipid in a semicontinuous or continuous culture system.Further additionally or alternatively, a mutant microorganism asprovided herein, e.g., a mutant microorganism having attenuatedexpression of a gene encoding a polypeptide of the Zn(II)2Cys6 familythat produces at least about 50% of the biomass and at least about 50%more lipid than is produced by a control microorganism cultured underthe same conditions, where the conditions support daily biomassaccumulation by the control microorganism, can have a higher carbon tonitrogen (C:N) ratio than a control microorganism. For example, the C:Nratio can be from about 1.5 to about 2.5 the C:N ratio of a controlmicroorganism when the mutant microorganism and the controlmicroorganism are cultured under conditions in which both the mutant andthe control microorganisms accumulate biomass, and the mutant producesat least 50%, at least 60%, at least 70%, at least 80%, at least 90% orat least 100% more lipid that the control microorganism and at least50%, at least 60%, at least 70%, at least 80%, or at least 85% of theTOC of the control microorganism.

The gene whose expression is attenuated in a mutant that has higherlipid productivity than a control microorganism can be a gene encoding apolypeptide of the Zn(II)2Cys6 family that has at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, or at least 95% identity to SEQ IDNO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9,SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14,SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, or SEQ ID NO:18. Alternativelyor in addition, the gene whose expression is attenuated can encode apolypeptide having a PAS3 domain (pfam08447), such as, for example, aPAS3 domain having at least at least 55%, at least 60%, at least 65%, atleast 70%, at least 75%, at least 80%, at least 85%, at least 90%, or atleast 95% identity to any of SEQ ID NOs:21-25.

A mutant microorganism as provided herein can be designed by targetingan endogenous gene of a microorganism of interest that encodes apolypeptide that includes a Zn2Cys6 domain as disclosed herein and/or aPAS3 domain as disclosed herein. Such genes can be identified in amicroorganism of interest by bioinformatics methods, molecular biologytechniques and combinations thereof. For example, a gene encoding apolypeptide that includes a Zn2Cys6 domain and/or a PAS3 domain can beidentified using Southern hybridization, screening of cDNA libraries byhybridization or PCR, for example, using degenerate probes and/orprimers. Genome sequences available in public or proprietary databasescan be searched by any of a number of programs that perform sequencematching (blast programs) or analyze domain structures of encoded aminoacid sequences. For example, hmmer.org provides software for analyzingstructural and functional domains encoded by genes that can be used toscan genome sequences, including, for example, hmmsearch and hmmscan.Such searches can be done online. Programs such as MUSCLE and hmmaligncan also be used to search for orthologs of proteins such as theproteins disclosed herein (e.g., ZnCys-2845 and orthologs) byconstructing phylogenetic trees to determine relationships amongproteins. In addition, sequence-based searches, including blastp,blastn, and tblastn (protein sequence queried against translatednucleotide sequence). Gene targeting can make use of the obtainedsequences from the genome of the microorganism of interest. It is notnecessary to resolve the complete structure of a gene to target the genefor attenuation. For example, using methods disclosed herein, including,without limitation, cas/CRISPR genome editing, RNAi constructs,antisense constructs, homologous recombination constructs, and ribozymeconstructs, only a portion of a gene sequence can be employed in geneattenuation constructs and techniques.

Gene Attenuation

A mutant microorganism having attenuated expression of a gene thatregulates lipid biosynthesis can be a mutant generated by any feasiblemethod, including but not limited to UV irradiation, gamma irradiation,or chemical mutagenesis, and screening for mutants having increase lipidproduction, for example using the assays disclosed herein or by stainingwith lipophilic dyes such as Nile Red or BODIPY (e.g., Cabanelas et al.(2015) Bioresource Technology 184:47-52). Methods for generating mutantsof microbial strains are well-known.

A mutant as provided herein that produces at least 25% more lipid whileproducing at least 50% of the biomass as the progenitor cell can also bea genetically engineered mutant, for example, a mutant in which aregulatory gene such as Zn(2)-C(6) fungal-type DNA-binding domainprotein (e.g., ZnCys-2845 or an ortholog thereof, e.g., a gene encodinga polypeptide having at least 55%, at least 60%, at least 65%, at least70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least95% identity to SEQ ID NO:2 or any of SEQ ID NOs:5-18) has been targetedby homologous recombination for knock-out or gene replacement (forexample with mutated form of the gene that encodes a polypeptide havingreduced activity with respect to the wild type polypeptide). Forexample, a microbial strain of interest may be engineered by sitedirected homologous recombination to insert a sequence into a genomiclocus and thereby alter a gene and/or its expression, where theinsertion can be, as nonlimiting examples, in the coding region of thegene, in an intron of the gene, in the 3′ UTR or the gene, in the 5′ UTRof the gene, or upstream of the transcriptional start site, i.e., in thepromoter region of the gene.

For example, gene knockout or replacement by homologous recombinationcan be by transformation of a homologous recombination nucleic acidconstruct, i.e., a nucleic acid (e.g., DNA) fragment that includes asequence homologous to the region of the genome to be altered, where thehomologous sequence is interrupted by a foreign sequence, typically butnot necessarily by a selectable marker gene that allows selection forthe integrated construct. The genome-homologous flanking sequences oneither side of the foreign sequence or mutated gene sequence can be forexample, at least 20, at least 50, at least 100, at least 200, at least300, at least 400, at least 500, at least 600, at least 700, at least800, at least 900, at least 1,000, at least 1,200, at least 1,500, atleast 1,750, or at least 2,000 nucleotides in length. A gene knockout orgene “knock in” construct in which a foreign sequence is flanked bytarget gene sequences, can be provided in a vector that can optionallybe linearized, for example, by cleavage at a site outside of the regionthat is to undergo homologous recombination, or can be provided as alinear fragment that is not in the context of a vector, for example, theknock-out or knock-in construct can be an isolated or synthesizedfragment, including but not limited to a PCR product. In some instances,a split marker system can be used to generate gene knock-outs byhomologous recombination, where two DNA fragments can be introduced thatcan regenerate a selectable marker and disrupt the gene locus ofinterest via three crossover events (Jeong et al. (2007) FEMS MicrobialLett 273: 157-163).

In one aspect the invention provides genetically modified organisms,e.g., microorganisms having one or more genetic modifications forattenuating expression of a lipid regulator gene such as a gene encodinga Zn(2)-C(6) fungal-type DNA-binding domain protein, that additionallymay have at least 55% identity to any of SEQ ID NO:2 or SEQ ID NOs:5-18.As used herein “attenuating expression of a lipid regulator gene” meansreducing or eliminating expression of the gene in any manner thatreduces production of the fully functional lipid regulator protein. Asused herein, “lipid regulator gene” refers to a gene whose attenuatedexpression in an organism or cell results in altered regulation of atleast 50, at least 100, at least 200, or at least 300 genes in theorganism or cell with respect to a control organism or cell and resultsin altered lipid productivity by the organism or cell. In an exemplaryembodiment, a lipid regulator gene is a gene encoding a Zn(2)-C(6)fungal-type DNA-binding domain protein. Means for attenuating a lipidregulator gene include, for example, homologous recombinationconstructs; CRISPR systems, including one or more guide RNAs, a casenzyme such but not limited to a Cas9 enzyme or a gene encoding a casenzyme, and optionally, one or more donor fragments for insertion into atargeted site; RNAi constructs; shRNAs; antisense RNA constructs;ribozyme constructs; TALENS or genes encoding TALENs, Zinc Fingernucleases or genes encoding Zinc Finger nucleases; and meganucleases orgenes encoding Zinc Finger nucleases.

For example, a recombinant microorganism engineered to have attenuatedexpression of a lipid regulator gene can have a disrupted lipidregulator gene that includes as least one insertion, mutation, ordeletion that reduces or abolishes expression of the gene such that afully functional lipid regulator gene is not produced or is produced inlower amounts than is produced by a control microorganism that does notinclude a disrupted lipid regulator gene. The disrupted lipid regulatorgene can be disrupted by, for example, an insertion or gene replacementmediated by homologous recombination and/or by the activity of ameganuclease, zinc finger nuclease (Perez-Pinera et al. (2012) Curr.Opin. Chem. Biol. 16: 268-277), TALEN (WO 2014/207043; WO 2014/076571),or a cas protein (e.g., a Cas9 protein) of a CRISPR system.

CRISPR systems, reviewed recently by Hsu et al. (Cell 157:1262-1278,2014) include, in addition to the cas nuclease polypeptide or complex, atargeting RNA, often denoted “crRNA”, that interacts with the genometarget site by complementarity with a target site sequence, atrans-activating (“tracr”) RNA that complexes with the cas polypeptideand also includes a region that binds (by complementarity) the targetingcrRNA.

The invention contemplates the use of two RNA molecules (a “crRNA” and a“tracrRNA”) that can be co-transformed into a host strain (or expressedin a host strain) that expresses or is transfected with a cas proteinfor genome editing, or the use of a single guide RNA that includes asequence complementary to a target sequence as well as a sequence thatinteracts with a cas protein. That is, in some strategies a CRISPRsystem as used herein can comprise two separate RNA molecules (a“tracr-RNA” and a “targeter-RNA” or “crRNA”, see below) and referred toherein as a “two RNA molecule CRISPR system” “two RNA guide system” or a“Split guide RNA system”. Alternatively, as illustrated in the examples,the DNA-targeting RNA can also include the trans-activating sequence forinteraction with the cas protein (in addition to the target-homologous(“cr”) sequences), that is, the DNA-targeting RNA can be a single RNAmolecule and is referred to herein as a “chimeric guide RNA,” a“single-guide RNA,” or an “sgRNA.” The terms “DNA-targeting RNA” and“gRNA” are inclusive, referring both to a two RNA guide system and tosingle-molecule DNA-targeting RNAs (i.e., sgRNAs). Both single-moleculeguide RNAs and two RNA guide systems have been described in detail inthe literature and for example, in U.S. Patent Application PublicationNo. US 2014/0068797, incorporated by reference herein in its entirety,and both are considered herein.

Any cas protein can be used in the methods herein, such as but notlimited to, Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9(also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2,Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4,Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3,Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, homologs thereof, or modifiedversions thereof. The cas protein can be a Cas9 protein, such as a Cas9protein of Staphylococcus pyogenes, S. thermophilus, S. pneumonia, S.aureus, or Neisseria meningitidis, as nonlimiting examples. Alsoconsidered are the Cas9 proteins provided as SEQ ID NOs:1-256 and795-1346 in U.S. Patent Application Publication No. US 2014/0068797, andchimeric Cas9 proteins that may combine domains from more than one cas9protein, as well variants and mutants of identified Cas9 proteins. Inadditional examples, a cas protein used for genome modification can be aCpf1 protein that uses a single RNA guide system, such as but notlimited to a Cpf1 protein of Acidaminococcus or Lachnospiraceae (see forexample Fagerlund et al. (2015) Genome Biol. 15:261; Zetsche et al.(2015) Cell 163:1-13); and European patent application EP3009511), aswell as the C2c1, C2c2, C2c3 RNA-guided nucleases (Shmakov et al. (2015)Molecular Cell 60: 1-13).

Cas nuclease activity cleaves target DNA to produce double strandbreaks. These breaks are then repaired by the cell in one of two ways:non-homologous end joining or homology-directed repair. Innon-homologous end joining (NHEJ), the double-strand breaks are repairedby direct ligation of the break ends to one another. In this case, nonew nucleic acid material is inserted into the site, although somenucleic acid material may be lost, resulting in a deletion, or altered,often resulting in mutation. In homology-directed repair, a donorpolynucleotide (sometimes referred to as a “donor DNA” or “editing DNA”)which may have homology to the cleaved target DNA sequence is used as atemplate for repair of the cleaved target DNA sequence, resulting in thetransfer of genetic information from the donor polynucleotide to thetarget DNA. As such, new nucleic acid material may be inserted/copiedinto the site. The modifications of the target DNA due to NHEJ and/orhomology-directed repair (for example using a donor DNA molecule) canlead to, for example, gene correction, gene replacement, gene tagging,transgene insertion, nucleotide deletion, gene disruption, genemutation, etc.

In some instances, cleavage of DNA by a site-directed modifyingpolypeptide (e.g., a cas nuclease, zinc finger nuclease, meganuclease,or TALEN) may be used to delete nucleic acid material from a target DNAsequence by cleaving the target DNA sequence and allowing the cell torepair the sequence in the absence of an exogenously provided donorpolynucleotide. Such NHEJ events can result in mutations (“mis-repair”)at the site of rejoining of the cleaved ends that can resulting in genedisruption.

Alternatively, if a DNA-targeting RNA is co-administered to cells thatexpress a cas nuclease along with a donor DNA, the subject methods maybe used to add, i.e., insert or replace, nucleic acid material to atarget DNA sequence (e.g., “knock out” by insertional mutagenesis, or“knock in” a nucleic acid that encodes a protein (e.g., a selectablemarker and/or any protein of interest), an siRNA, an miRNA, etc., tomodify a nucleic acid sequence (e.g., introduce a mutation), and thelike.

A donor DNA can in particular embodiments include a gene regulatorysequence (e.g., a promoter) that can, using CRISPR targeting, beinserted upstream of the coding regions of the gene and upstream of thepresumed proximal promoter region of the gene, for example, at least 50bp, at least 100 bp, at least 120 bp, at least 150 bp, at least 200 bp,at least 250 bp, at least 300 bp, at least 350 bp, at least 400 bp, atleast 450 bp, or at least 500 bp upstream of the initiating ATG of thecoding region of the lipid regulator gene. The donor DNA can include asequence, such as for example a selectable marker or any convenientsequence, that may be interfere with the native promoter. The additionalsequence inserted upstream of the initiating ATG of the lipid regulatoropen reading frame (e.g., in the 5′UTR or upstream of thetranscriptional start site of the lipid regulator gene) can decrease oreven eliminate expression of the endogenous lipid regulator gene.Alternatively or in addition, the native lipid regulator gene can haveits endogenous promoter wholly or partially replaced by a weaker ordifferently regulated promoter, or a non-promoter sequence.

In some examples, a nucleic acid molecule introduced into a host cellfor generating a high efficiency genome editing cell line encodes a cas9enzyme that is mutated to with respect to the corresponding wild-typeenzyme such that the mutated cas9 enzyme lacks the ability to cleave oneor both strands of a target polynucleotide containing a target sequence.For example, an aspartate-to-alanine substitution (D10A) in the RuvC Icatalytic domain of Cas9 from S. pyogenes converts Cas9 from a nucleasethat cleaves both strands to a nickase (an enzyme that cleaves a singlestrand). Other examples of mutations that render Cas9 a nickase include,without limitation, H840A, N854A, and N863A. In some embodiments, a Cas9nickase may be used in combination with guide sequence(s), e.g., twoguide sequences, which target respectively sense and antisense strandsof the DNA target. This combination allows both strands to be nicked andused to induce NHEJ. Two nickase targets (within close proximity buttargeting different strands of the DNA) can be used to inducingmutagenic NHEJ. Such targeting of a locus using enzymes that cleaveopposite strains at staggered positions can also reduce nontargetcleavage, as both strands must be accurately and specifically cleaved toachieve genome mutation.

In additional examples, a mutant cas9 enzyme that is impaired in itsability to cleave DNA can be expressed in the cell, where one or moreguide RNAs that target a sequence upstream of the transcriptional ortranslational start site of the targeted gene are also introduced. Inthis case, the cas enzyme may bind the target sequence and blocktranscription of the targeted gene (Qi et al. (2013) Cell152:1173-1183). This CRISPR interference of gene expression can bereferred to as RNAi and is also described in detail in Larson et al.(2013) Nat. Protoc. 8: 2180-2196.

In some cases, a cas polypeptide such as a Cas9 polypeptide is a fusionpolypeptide, comprising, e.g.: i) a Cas9 polypeptide (which canoptionally be variant Cas9 polypeptide as described above); and b) acovalently linked heterologous polypeptide (also referred to as a“fusion partner”). A heterologous nucleic acid sequence may be linked toanother nucleic acid sequence (e.g., by genetic engineering) to generatea chimeric nucleotide sequence encoding a chimeric polypeptide. In someembodiments, a Cas9 fusion polypeptide is generated by fusing a Cas9polypeptide with a heterologous sequence that provides for subcellularlocalization (i.e., the heterologous sequence is a subcellularlocalization sequence, e.g., a nuclear localization signal (NLS) fortargeting to the nucleus; a mitochondrial localization signal fortargeting to the mitochondria; a chloroplast localization signal fortargeting to a chloroplast; an ER retention signal; and the like). Insome embodiments, the heterologous sequence can provide a tag (i.e., theheterologous sequence is a detectable label) for ease of tracking and/orpurification (e.g., a fluorescent protein, e.g., green fluorescentprotein (GFP), YFP, RFP, CFP, mCherry, tdTomato, and the like; ahemagglutinin (HA) tag; a FLAG tag; a Myc tag; and the like).

Host cells can be genetically engineered (e.g., transduced ortransformed or transfected) with, for example, a vector construct thatcan be, for example, a vector for homologous recombination that includesnucleic acid sequences homologous to a portion of a lipid regulator genelocus of the host cell or to regions adjacent thereto, or can be anexpression vector for the expression of any or a combination of: a casprotein (e.g., a cas9 protein), a CRISPR chimeric guide RNA, a crRNA,and/or a tracrRNA, an RNAi construct (e.g., a shRNA), an antisense RNA,or a ribozyme. The vector can be, for example, in the form of a plasmid,a viral particle, a phage, etc. A vector for expression of a polypeptideor RNA for genome editing can also be designed for integration into thehost, e.g., by homologous recombination. A vector containing apolynucleotide sequence as described herein, e.g., sequences havinghomology to host lipid regulator gene sequences (including sequencesthat are upstream and downstream of the lipid regulator-encodingsequences), as well as, optionally, a selectable marker or reportergene, can be employed to transform an appropriate host to causeattenuation of a lipid regulator gene.

The recombinant microorganism in some examples can have reduced but notabolished expression of the lipid regulator gene, and the recombinantmicroorganism can have an increase in lipid production of from about 25%to about 200% or more, for example. A genetically modified microorganismas provided herein can in some examples include a nucleic acid constructfor attenuating the expression of a lipid regulator gene, such as, forexample, a gene encoding a polypeptide having at least 55%, at least60%, at least 65%, at least 70%, at least 75%, at least 80%, at least85%, at least 90%, or at least 95% identity to SEQ ID NO:2 or any of SEQID NO:5-18. For example, a host microorganism can include a constructfor expressing an RNAi molecule, ribozyme, or antisense molecule thatreduces expression of a lipid regulator gene encoding a polypeptidehaving at least 55% identity to SEQ ID NO:2 or any of SEQ ID NO:5-18. Insome examples, a recombinant microorganism as provided herein caninclude at least one introduced (exogenous or non-native) construct forreducing expression of a lipid regulator gene.

In some examples, engineered strains can be selected for expression of alipid regulator gene that is decreased with respect to a control cellthat does not include a genetic modification for attenuating lipidregulator gene expression, but not eliminated, using methods known inthe art, such as, for example, RNA-Seq or reverse transcription-PCR(RT-PCR).

A genetically engineered strain as provided herein can be engineered toinclude a construct for attenuating gene expression by reducing theamount, stability, or translatability of mRNA of a gene encoding a lipidregulator. For example, a microorganism such as an algal or heterokontstrain can be transformed with an antisense RNA, RNAi, or ribozymeconstruct targeting an mRNA of a lipid regulator gene using methodsknown in the art. For example, an antisense RNA construct that includesall or a portion of the transcribed region of a gene can be introducedinto a microorganism to decrease gene expression (Shroda et al. (1999)The Plant Cell 11:1165-78; Ngiam et al. (2000) Appl. Environ. Microbiol.66: 775-782; Ohnuma et al. (2009) Protoplasma 236: 107-112; Lavaud etal. (2012) PLoS One 7:e36806). Alternatively or in addition, an RNAiconstruct (for example, a construct encoding a short hairpin RNA)targeting a gene having a Zn(2)Cys(6) domain can be introduced into amicroorganism such as an alga or heterokont for reducing expression ofthe lipid regulator gene (see, for example, Cerruti et al. (2011)Eukaryotic Cell (2011) 10: 1164-1172; Shroda et al. (2006) Curr. Genet.49:69-84).

Ribozymes are RNA-protein complexes that cleave nucleic acids in asite-specific fashion. Ribozymes have specific catalytic domains thatpossess endonuclease activity. For example, U.S. Pat. No. 5,354,855reports that certain ribozymes can act as endonucleases with a sequencespecificity greater than that of known ribonucleases and approachingthat of the DNA restriction enzymes. Catalytic RNA constructs(ribozymes) can be designed to base pair with an mRNA encoding a gene asprovided herein to cleave the mRNA target. In some examples, ribozymesequences can be integrated within an antisense RNA construct to mediatecleavage of the target. Various types of ribozymes can be considered,their design and use is known in the art and described, for example, inHaseloff et al. (1988) Nature 334:585-591.

Ribozymes are targeted to a given sequence by virtue of annealing to asite by complimentary base pair interactions. Two stretches of homologyare required for this targeting. These stretches of homologous sequencesflank the catalytic ribozyme structure defined above. Each stretch ofhomologous sequence can vary in length from 7 to 15 nucleotides. Theonly requirement for defining the homologous sequences is that, on thetarget RNA, they are separated by a specific sequence which is thecleavage site. For hammerhead ribozyme, the cleavage site is adinucleotide sequence on the target RNA is a uracil (U) followed byeither an adenine, cytosine or uracil (A, C or U) (Thompson et al.,(1995) Nucl Acids Res 23:2250-68). The frequency of this dinucleotideoccurring in any given RNA is statistically 3 out of 16. Therefore, fora given target messenger RNA of 1,000 bases, 187 dinucleotide cleavagesites are statistically possible.

The general design and optimization of ribozyme directed RNA cleavageactivity has been discussed in detail (Haseloff and Gerlach (1988)Nature 334:585-591; Symons (1992) Ann Rev Biochem 61: 641-71; Chowriraet al. (1994) J Biol Chem 269:25856-64; Thompson et al. (1995) supra),all incorporated by reference in their entireties. Designing and testingribozymes for efficient cleavage of a target RNA is a process well knownto those skilled in the art. Examples of scientific methods fordesigning and testing ribozymes are described by Chowrira et al., (1994)supra and Lieber and Strauss (1995) Mol Cell Biol. 15: 540-51, eachincorporated by reference. The identification of operative and preferredsequences for use in down regulating a given gene is a matter ofpreparing and testing a given sequence, and is a routinely practiced“screening” method known to those of skill in the art.

The use of RNAi constructs is described in literature cited above aswell as in US2005/0166289 and WO 2013/016267, for example. A doublestranded RNA with homology to the target gene is delivered to the cellor produced in the cell by expression of an RNAi construct, for example,an RNAi short hairpin (sh) construct. The construct can include asequence that is identical to the target gene, or at least 70%, 80%,90%, 95%, or between 95% and 100% identical to a sequence of the targetgene. The construct can have at least 20, at least 30, at least 40, atleast 50, at least 100, at least 200, at least 300, at least 400, atleast 500, at least 600, at least 700, at least 800, at least 900, or atleast 1 kb of sequence homologous to the target gene. Expression vectorscan be engineered using promoters selected for continuous or inducibleexpression of an RNAi construct, such as a construct that produces anshRNA.

A nucleic acid construct for gene attenuation, e.g., a ribozyme, RNAi,or antisense construct can include at least fifteen, at least twenty, atleast thirty, at least forty, at least fifty, or at least sixtynucleotides having at least 80% identity, such as at least 85%, at least90%, at least 95%, or at least 99% or complementarity to at least aportion of the sequence of an endogenous lipid regulator gene of themicroorganism to be engineered. A nucleic acid construct for geneattenuation, e.g., a ribozyme, RNAi, or antisense construct can includeat least fifteen, at least twenty, at least thirty, at least forty, atleast fifty, or at least sixty nucleotides having at least 80%, such asat least 95% or about 100%, identity or complementarity to the sequenceof a naturally-occurring gene, such as a gene having encoding apolypeptide having at least 50%, at least 55%, at least 60%, at least65%, at least 70%, at least 75%, at least 80% or at least 85%, at least90%, or at least 95% sequence identity to an endogenous lipid regulatorgene. For example, a nucleic acid construct for gene attenuation, e.g.,a ribozyme, RNAi, or antisense construct can include at least fifteen,at least twenty, at least thirty, at least forty, at least fifty, or atleast sixty nucleotides having at least 80% identity or complementarityto the sequence of a naturally-occurring lipid regulator gene, such asany provided herein. The nucleotide sequence can be, for example, fromabout 30 nucleotides to about 3 kilobases or greater, for example, from30-50 nucleotides in length, from 50 to 100 nucleotides in length, from100 to 500 nucleotides in length, from 500 nucleotides to 1 kb inlength, from 1 kb to 2 kb in length, or from 2 to 5 kb. For example, anantisense sequence can be from about 100 nucleotides to about 1 kb inlength. For example, a nucleic acid construct for gene attenuation,e.g., a ribozyme, RNAi, or antisense construct can include at leastfifteen, at least twenty, at least thirty, at least forty, at leastfifty, at least sixty, or at least 100 nucleotides having at least 50%,at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, atleast 80%, or at least 85%, for example at least 86%, at least 87%, atleast 88%, at least 89%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, or at least 95% identity or complementarity toan endogenous lipid regulator gene or a portion thereof.

Promoters used in antisense, RNAi, or ribozyme constructs can be anythat are functional in the host organism and that are suitable for thelevels of expression required for reducing expression of the target geneto a desired amount. Promoters functional in algae and heterokonts areknown in the art and disclosed herein. The construct can be transformedinto algae using any feasible method, include any disclosed herein. Arecombinant organism or microorganism transformed with a nucleic acidmolecule for attenuating lipid regulator gene expression, such as butnot limited to an antisense, RNAi, or ribozyme construct, can have theproperties of a lipid regulator mutant as described herein, including,for example, reduced chlorophyll, increased photosynthetic efficiency,and increased productivity in culture, with respect to a host organismor microorganism that does not include the exogenous nucleic acidmolecule that results in attenuated gene expression.

In additional examples, such as disclosed in Examples herein, geneattenuation that decreases but does not eliminate expression of thetarget gene can be achieved through the use of homologous recombinationor CRISPR/Cas9 genome editing where the donor fragment is targeted forinsertion into a non-coding region of a gene. For example, a selectablemarker cassette or other donor fragment can be targeted by the use of anappropriate guide RNA to the 5′ UTR, 3′ UTR, or an intron of a genewhose reduced expression is desired. Thus, another aspect of theinvention is a method for attenuating expression of a gene the includesinserting a nucleic acid fragment into a site upstream of thetranslational start site or downstream of a translational terminationsite, wherein the expression level of the gene is reduced. Asnonlimiting examples, a donor fragment insertion can be introduced intoa region up to 2 kb upstream of the translational start site of a gene,or up to 2 kb downstream of the termination codon of a gene. Forexample, an insertion that is targeted to a site of between about 5 bpand 2 kb upstream of the translational start site, or between about 10bp and 1.5 kb upstream of the translational start site, or between about10 bp and about 1.2 kb upstream of the translational start site, orbetween about 20 bp and about 1 kb upstream of the translational startsite. Alternatively or in addition, an insertion can be targeted to the3′ UTR of a gene. Alternatively or in addition, an insertion that istargeted to a site of between about 5 bp and 2 kb downstream of thetranslational termination site (stop codon), or between about 10 bp and1.5 kb downstream of the stop codon, or between about 10 bp and about1.2 kb downstream of the stop codon, or between about 20 bp and about 1kb downstream of the stop codon. Without being limited to any particularmechanism, such insertions may reduce the rate or transcription of agene or may reduce the stability of a resulting transcript.

Nucleic Acid Molecules and Constructs

Also provided herein are nucleic acid molecules encoding polypeptidesthat include amino acid sequences having at least 60%, at least 65%, atleast 70%, or at least 75%, at least 80%, at least 85%, at least 90%, orat least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ IDNO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ IDNO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ IDNO:17. Alternatively or in addition, a nucleic acid molecule as providedherein can include a sequence having at least 50%, at least 55%, atleast 60%, at least 65%, at least 70%, at least 75%, at least 80%, atleast 85%, at least 90%, or at least 95% identity to SEQ ID NO:1 or anyof SEQ ID NOs:72-84. The polypeptide having at least 60% identity to anamino acid sequence selected from the group consisting of SEQ ID NO:2and SEQ ID NOs:5-17 or encoded by SEQ ID NO:1 or any of SEQ ID NOs:72-84can include an amino acid sequence encoding a Zn(2)Cys(6) domain, e.g.,a domain belonging to pfam PF00172. For example, the polypeptide encodedby the nucleic acid molecule can include a Zn(2)Cys(6) domain having anamino acid sequence with at least 60%, at least 65%, at least 70%, or atleast 75%, at least 80%, at least 85%, at least 90%, or at least 95%identity to SEQ ID NO:3. Alternatively or in addition, a polypeptideencoded by a nucleic acid molecule as provided herein can optionallyfurther include a PAS (or PAS3) domain. For example a polypeptideencoded by a nucleic acid molecule as provided herein can include a PASdomain having at least 60%, at least 65%, at least 70%, or at least 75%,at least 80%, at least 85%, at least 90%, or at least 95% identity toany of SEQ ID NO:21-SEQ ID NO:25.

The nucleic acid molecule in various examples can be or comprise a cDNAthat lacks one or more introns present in the naturally-occurring gene,or, alternatively, can include one or more introns not present in thenaturally-occurring gene. The nucleic acid molecule in various examplescan have a sequence that is not 100% identical to a naturally-occurringgene. For example, the nucleic acid molecule can include a mutation withrespect to a naturally-occurring gene that reduces the activity of theencoded polypeptide or reduces expression of the mRNA or protein encodedby the gene.

The nucleic acid molecule in various examples can comprise aheterologous promoter operably linked to the sequence encoding apolypeptide that includes an amino acid sequence having at least 60%, atleast 65%, at least 70%, or at least 75%, at least 80%, at least 85%, atleast 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ IDNO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11,SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, orSEQ ID NO:17 and/or can comprise a heterologous promoter operably linkedto a sequence having at least 50%, at least 55%, at least 60%, at least65%, at least 70%, at least 75%, at least 80%, at least 85%, at least90%, or at least 95% identity to SEQ ID NO:1 or any of SEQ ID NOs:72-84.Alternatively or in addition, a nucleic acid molecule can comprise avector that includes a sequence encoding a polypeptide that includes anamino acid sequence having at least 60%, at least 65%, at least 70%, orat least 75%, at least 80%, at least 85%, at least 90%, or at least 95%identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ IDNO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ IDNO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17 and/orhas at least 50%, at least 55%, at least 60%, at least 65%, at least70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least95% identity to SEQ ID NO:1 or any of SEQ ID NOs:72-84.

A further aspect of the invention is a construct designed forattenuating expression of a gene encoding a Zn(2)Cys(6) DNA-bindingdomain polypeptide. The construct can be or comprise, in variousexamples, a sequence encoding a guide RNA of a CRISPR system, an RNAiconstruct, an antisense construct, a ribozyme construct, or a constructfor homologous recombination, e.g., a construct having one or morenucleotide sequences having homology to a naturally-occurringZn(2)Cys(6) domain-encoding gene as disclosed herein and/or sequencesadjacent thereto in the native genome from which the gene is derived.For example, the construct can include at least a portion of a geneencoding a polypeptide having a Zn(2)Cys(6) domain, e.g., a sequencehomologous to at least a portion of an gene that encodes a polypeptidethat includes an amino acid sequence having at least 60%, at least 65%,at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%,or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ IDNO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ IDNO:17 or can include at least a portion of a nucleic acid sequencehaving at least 50%, at least 55%, at least 60%, at least 65%, at least70%, or at least 75%, at least 80%, at least 85%, at least 90%, or atleast 95% identity to SEQ ID NO:1 or any of SEQ ID NOs:72-84.

The construct for gene attenuation can include, for example, at least aportion of the coding region of a gene encoding a polypeptide having aZn(2)Cys(6) domain or a polypeptide having at least 60% identity to anyof SEQ ID NO:2 and SEQ ID NOs:5-17 or at least a portion of a genehaving at least 50% identity to SEQ ID NO:1 or any of SEQ ID NOs:72-84,at least a portion of an intron of a gene encoding a polypeptide havinga Zn(2)Cys(6) domain or a polypeptide having at least 60% identity toany of SEQ ID NO:2 and SEQ ID NOs:5-17, at least a portion of a 5′UTR ofa gene encoding a polypeptide having a Zn(2)Cys(6) domain or apolypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQID NOs:5-17, at least a portion of the promoter region of a geneencoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptidehaving at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17,and/or at least a portion of a 3′ UTR of a gene encoding a polypeptidehaving a Zn(2)Cys(6) domain or a polypeptide having at least 60%identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17. In some examples,the construct can be an RNAi, ribozyme, or antisense construct and caninclude a sequence from the transcribed region of the gene encoding apolypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17 in either senseor antisense orientation.

In further examples a construct can be designed for the in vitro or invivo expression of a guide RNA (e.g., of a CRISPR system) designed totarget a gene having a sequence having at least 50%, at least 55%, atleast 60%, at least 65%, at least 70%, or at least 75%, at least 80%, atleast 85%, at least 90%, or at least 95% identity to at least a portionof SEQ ID NO:1 or any of SEQ ID NOs:72-84 or coding a polypeptide havinga Zn(2)Cys(6) domain or a polypeptide having at least 60% identity toany of SEQ ID NO:2 and SEQ ID NOs:5-17, and can include a sequencehomologous to a portion of a gene encoding a polypeptide having aZn(2)Cys(6) domain or a polypeptide having at least 60% identity to anyof SEQ ID NO:2 and SEQ ID NOs:5-17, including, for example, an intron, a5′UTR, a promoter region, and/or a 3′ UTR of a gene encoding apolypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17. In yet furtherexamples, a construct for attenuating expression a gene encoding aZn(2)Cys(6) domain-containing polypeptide can be a guide RNA orantisense oligonucleotide, where the sequence having homology to atranscribed region of a gene encoding a polypeptide having a Zn(2)Cys(6)domain in antisense orientation.

Further provided are guide RNAs for attenuating expression of aZn(2)Cys(6) gene or a gene encoding a polypeptide having at least 60%identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, and DNA constructsencoding such guide RNAs. The guide RNAs can be chimeric or single guideRNAs or can be guide RNAs that include a tracr mate sequence but requirean additional tracr RNA to effect genome editing. In variousembodiments, provided herein is a nucleic acid molecule having at least50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least75%, at least 80%, at least 85%, at least 90%, or at least 95% identityto at least a portion of SEQ ID NO:1 or any of SEQ ID NOs:72-84, wherethe nucleic acid molecule encodes a guide RNA of a CRISPR system, thatcan be, as nonlimiting examples, a Cas9/CRISPR system or a Cpf1 CRISPRsystem. The nucleic acid molecule can include, for example at least 17,at least 18, at least 19, at least 20, at least 21, at least 22, atleast 23, at least 24, or at least 25 nucleotides of sequence of anaturally occurring Zn(2)Cys(6) gene, such as SEQ ID NO:1 or any of SEQID NOs:72-84. In exemplary embodiments, the guide RNA or nucleic acidsequence encoding the guide RNA can include any of SEQ ID NOs:51-62 orsequences having at least 88% or 93% identity to any thereof.

In addition, provided herein are antisense, ribozyme, or RNAi constructsthat include at least a portion of a gene having encoding a Zn(2)Cys(6)or a polypeptide having at least 60% identity to any of SEQ ID NO:2 andSEQ ID NOs:5-17, in which a promoter, such as a heterologous promoter,is operably linked to the Zn(2)Cys(6) gene sequence and the Zn(2)Cys(6)gene sequence is in antisense orientation.

Further, provided herein are constructs for homologous recombinationthat include at least one sequence from a Zn(2)Cys(6) gene locus of thegenome of an alga juxtaposed with a heterologous nucleic acid sequencethat can be, in nonlimiting examples, a selectable marker or detectablemarker gene. In some examples a construct for homologous recombinationincludes two nucleic acid sequences from a Zn(2)Cys(6) gene locus of thegenome of an alga where the two sequences flank a heterologous sequencefor insertion into the Zn(2)Cys(6) gene locus.

One skilled in the art will appreciate that a number of transformationmethods can be used for genetic transformation of microorganisms and,therefore, can be deployed for the methods of the present invention.“Stable transformation” is intended to mean that the nucleic acidconstruct introduced into an organism integrates into the genome of theorganism or is part of a stable episomal construct and is capable ofbeing inherited by the progeny thereof “Transient transformation” isintended to mean that a polynucleotide is introduced into the organismand does not integrate into the genome or otherwise become establishedand stably inherited by successive generations.

Genetic transformation can result in stable insertion and/or expressionof transgenes, constructs from either the nucleus or the plastid, and insome cases can result in transient expression of transgenes. Thetransformation methods can also be used for the introduction of guideRNAs or editing DNAs. Genetic transformation of microalgae has beenreported successful for more than 30 different strains of microalgae,which belong to at least ˜22 species of green, red, and brown algae,diatoms, euglenids, and dianoflagellates (see, e.g., Radakovits et al.,Eukaryotic Cell, 2010; and Gong et al., J. Ind. Microbiol. Biotechnol.,2011). Non-limiting examples of such useful transformation methodsinclude agitation of cells in the presence of glass beads or siliconcarbide whiskers as reported by, for example, Dunahay, Biotechniques,15(3):452-460, 1993; Kindle, Proc. Natl. Acad. Sci. U.S.A., 1990;Michael and Miller, Plant J., 13, 427-435, 1998. Electroporationtechniques have been successfully used for genetic transformation ofseveral microalgal species including Nannochloropsis sp. (see, e.g.,Chen et al., J. Phycol., 44:768-76, 2008), Chlorella sp. (see, e.g.,Chen et al., Curr. Genet., 39:365-370, 2001; Chow and Tung, Plant CellRep. Vol. 18, No. 9, 778-780, 1999), Chlamydomonas (Shimogawara et al.,Genetics, 148: 1821-1828, 1998), Dunaliella (Sun et al., Mol.Biotechnol., 30(3): 185-192, 2005). Micro-projectile bombardment, alsoreferred to as microparticle bombardment, gene gun transformation, orbiolistic bombardment, has been used successfully for several algalspecies including, for example, diatoms species such as Phaeodactylum(Apt et al., Mol. Gen. Genet., 252:572-579, 1996), Cyclotella andNavicula (Dunahay et al., J. Phycol., 31:1004-1012, 1995), Cylindrotheca(Fischer et al., J. Phycol., 35:113-120, 1999), and Chaetoceros sp.(Miyagawa-Yamaguchi et al., Phycol. Res. 59: 113-119, 2011), as well asgreen algal species such as Chlorella (El-Sheekh, Biologia Plantarum,Vol. 42, No. 2: 209-216, 1999), and Volvox species (Jakobiak et al.,Protist, 155:381-93, 2004). Additionally, Agrobacterium-mediated genetransfer techniques can also be useful for genetic transformation ofmicroalgae, as has been reported by, for example, Kumar, Plant Sci.,166(3):731-738, 2004, and Cheney et al., J. Phycol., Vol. 37, Suppl. 11,2001.

A transformation vector or construct as described herein will typicallycomprise a marker gene that confers a selectable or scorable phenotypeon target host cells, e.g., algal cells or may be co-transformed with aconstruct that includes a marker. A number of selectable markers havebeen successfully developed for efficient isolation of genetictransformants of algae. Common selectable markers include antibioticresistance, fluorescent markers, and biochemical markers. Severaldifferent antibiotic resistance genes have been used successfully forselection of microalgal transformants, including blastocydin, bleomycin(see, for example, Apt et al., 1996, supra; Fischer et al., 1999, supra;Fuhrmann et al., Plant J., 19, 353-61, 1999, Lumbreras et al., Plant J.,14(4):441-447, 1998; Zaslayskaia et al., J. Phycol., 36:379-386, 2000),spectinomycin (Cerutti et al., Genetics, 145: 97-110, 1997; Doetsch etal., Curr. Genet., 39, 49-60, 2001; Fargo, Mol. Cell. Biol., 19:6980-90,1999), streptomycin (Berthold et al., Protist, 153:401-412, 2002),paromomycin (Jakobiak et al., Protist, supra.; Sizova et al., Gene,277:221-229, 2001), nourseothricin (Zaslayskaia et al., 2000, supra),G418 (Dunahay et al., 1995, supra; Poulsen and Kroger, FEBS Lett.,272:3413-3423, 2005, Zaslayskaia et al., 2000, supra), hygromycin(Berthold et al., 2002, supra), chloramphenicol (Poulsen and Kroger,2005, supra), and many others. Additional selectable markers for use inmicroalgae such as Chlamydomonas can be markers that provide resistanceto kanamycin and amikacin resistance (Bateman, Mol. Gen. Genet.263:404-10, 2000), zeomycin and phleomycin (e.g., ZEOCIN™ pheomycin D1)resistance (Stevens, Mol. Gen. Genet. 251:23-30, 1996), and paramomycinand neomycin resistance (Sizova et al., 2001, supra). Other fluorescentor chromogenic markers that have been used include luciferase(Falciatore et al., J. Mar. Biotechnol., 1: 239-251, 1999; Fuhrmann etal., Plant Mol. Biol., 2004; Jarvis and Brown, Curr. Genet., 19:317-322, 1991), β-glucuronidase (Chen et al., 2001, supra; Cheney etal., 2001, supra; Chow and Tung, 1999, supra; El-Sheekh, 1999, supra;Falciatore et al., 1999, supra; Kubler et al., J. Mar. Biotechnol.,1:165-169, 1994), β-galactosidase (Gan et al., J. Appl. Phycol.,15:345-349, 2003; Jiang et al., Plant Cell Rep., 21:1211-1216, 2003; Qinet al., High Technol. Lett., 13:87-89, 2003), and green fluorescentprotein (GFP) (Cheney et al., 2001, supra; Ender et al., Plant Cell,2002, Franklin et al., Plant J., 2002; 56, 148, 210).

One skilled in the art will readily appreciate that a variety of knownpromoter sequences can be usefully deployed for transformation systemsof microalgal species in accordance with the present invention. Forexample, the promoters commonly used to drive transgene expression inmicroalgae include various versions of the of cauliflower mosaic viruspromoter 35S (CaMV35S), which has been used in both dinoflagellates andchlorophyta (Chow et al, Plant Cell Rep., 18:778-780, 1999; Jarvis andBrown, Curr. Genet., 317-321, 1991; Lohuis and Miller, Plant J.,13:427-435, 1998). The SV40 promoter from simian virus has also reportedto be active in several algae (Gan et al., J. Appl. Phycol., 151345-349, 2003; Qin et al., Hydrobiologia 398-399, 469-472, 1999). Thepromoters of RBCS2 (ribulose bisphosphate carboxylase, small subunit)(Fuhrmann et al., Plant J., 19:353-361, 1999) and PsaD (abundant proteinof photosystem I complex; Fischer and Rochaix, FEBS Lett 581:5555-5560,2001) from Chlamydomonas can also be useful. The fusion promoters ofHSP70A/RBCS2 and HSP70A/β2TUB (tubulin) (Schroda et al., Plant J.,21:121-131, 2000) can also be useful for an improved expression oftransgenes, in which HSP70A promoter may serve as a transcriptionalactivator when placed upstream of other promoters. High-level expressionof a gene of interest can also be achieved in, for example diatomsspecies, under the control of a promoter of an fcp gene encoding adiatom fucoxanthin-chlorophyll a/b binding protein (Falciatore et al.,Mar. Biotechnol., 1:239-251, 1999; Zaslayskaia et al. J. Phycol.36:379-386, 2000) or the vcp gene encoding a eustigmatophyteviolaxanthin-chlorophyll a/b binding protein (see U.S. Pat. No.8,318,482). If so desired, inducible promoters can provide rapid andtightly controlled expression of genes in transgenic microalgae. Forexample, promoter regions of the NR genes encoding nitrate reductase canbe used as such inducible promoters. The NR promoter activity istypically suppressed by ammonium and induced when ammonium is replacedby nitrate (Poulsen and Kroger, FEBS Lett 272:3413-3423, 2005), thusgene expression can be switched off or on when microalgal cells aregrown in the presence of ammonium/nitrate. Additional algal promotersthat can find use in the constructs and transformation systems providedherein include those disclosed in U.S. Pat. No. 8,883,993; U.S. PatentAppl. Pub. No. US 2013/0023035; U.S. Patent Application Pub. No. US2013/0323780; and U.S. Patent Application Pub. No. US 2014/0363892.

Host cells can be either untransformed cells or cells that are alreadytransfected with at least one nucleic acid molecule. For example, analgal host cell that is engineered to have attenuated expression of alipid regulator gene can further include one or more genes that mayconfer any desirable trait, such as, but not limited to, increasedproduction of biomolecules of interest, such as one or more proteins,pigments, alcohols, or lipids.

Methods of Producing Lipids

Also provided herein are methods of producing lipid by culturing amutant microorganism as provided herein that has increased lipidproductivity with respect to a control cell while producing at least 45%of the biomass produced by a control cell under the same cultureconditions. The methods include culturing a mutant microorganism asprovided herein in a suitable medium to produce lipid and recoveringbiomass or at least one lipid from the culture. The microorganism can insome examples be an alga, and the culture can be a photoautotrophicculture. Culturing can be in batch, semi-continuous, or continuous mode.

The mutant microorganism in some examples can be cultured in a mediumthat comprises less than about 5 mM ammonium, for example, less thanabout 2.5 mM ammonium, less than about 2 mM ammonium, less than about1.5 mM ammonium, less than or equal to about 1 mM ammonium, or less thanor equal to about 0.5 mM. The culture medium can include, for example,from about 0 to about 2.5 mM ammonium, from about 0.1 to about 2.5 mMammonium, from about 0.5 to about 2.5 mM ammonium, from about 0 to about1.5 mM ammonium, from about 0.1 to about 1 mM ammonium, or from about0.2 to about 1 mM ammonium. The microorganism can be cultured in amedium that includes nitrate, which in some examples may besubstantially the sole nitrogen source in the culture medium or may bepresent in addition to less than 5 mM ammonium, less than 2.5 mMammonium, less than 1.0 mM ammonium, or less than or equal to about 0.5mM ammonium. Alternatively or in addition, the culture medium cancomprises urea, which in some examples can be substantially the solesource of nitrogen in the culture medium.

Yet another aspect of the invention is a method of producing lipid thatincludes culturing a microorganism under conditions in which the FAME toTOC ratio of the microorganism is maintained between about 0.3 and about0.8, and isolating lipid from the microorganism, the culture medium, orboth. For example, the microorganisms can be cultured such that the FAMEto TOC ratio is maintained at between about 0.3 and about 0.8, betweenabout 0.4 and about 0.7, between about 0.4 and about 0.6, or betweenabout 0.45 and about 0.55. The ratio can be maintained at between about0.3 and about 0.8, for example between about 0.4 and about 0.8, betweenabout 0.4 and about 0.7, between about 0.4 and about 0.6, or betweenabout 0.45 and about 0.55 for at least 3, at least 4, at least 5, atleast 6, at least 7, at least 8, at least 9, at least 10, at least 11,at least 12, at least 13, at least 15, at least 20, at least 30 days, orat least 60 days. In these methods the microorganism can be culturedunder continuous or semi-continuous conditions. The method of producinglipid can include culturing a mutant microorganism such as any providedherein under conditions in which the FAME to TOC ratio of themicroorganism is maintained between about 0.3 and about 0.8, betweenabout 0.3 and about 0.8, between about 0.4 and about 0.7, between about0.4 and about 0.6, or between about 0.45 and about 0.55. For example,the microorganism can be a mutant microorganism having attenuatedexpression of a gene encoding a polypeptide having at least 55%, atleast 65%, at least 75%, or at least 85% identity to a polypeptidecomprising an amino acid sequence selected from the group consisting ofSEQ ID NO:2 and SEQ ID NOs:5-17. The FAME to TOC ratio may be adjusted,for example, by the type and concentration of nitrogen source present inthe culture medium. For example, the method may include culturing amicroorganism, such as a mutant microorganism as disclosed herein, in aculture medium that includes nitrate and less than 2.5 mM ammonium orless than 1.0 mM ammonium.

The culture conditions in the methods provided herein are preferablyconditions in which a control microorganism (i.e., a microorganism thatdoes not have the mutation leading to higher lipid productivity)produces biomass on a daily basis, for example, produces biomass on adaily basis for at least five, at least eight, at least ten, or at leasttwelve days, and in various embodiments the methods of producing lipidresult in the mutant microorganism producing at least 50% more lipidthan a control microorganism while exhibiting a decrease in biomass(e.g., TOC) accumulation of no more than 35%, 30%, 25%, 20%, 15%, 10%,5%, 2%, or 1% with respect to the control microorganism. For example,the methods of producing lipid can include culturing a mutantmicroorganism as provided herein in a suitable medium to produce lipidand recovering biomass or at least one lipid from the culture, in whichthe mutant microorganism produces at least 50%, at least 55%, at least60%, at least 65%, at least 70%, at least 75%, at least 80%, at least85%, at least 90%, at least 95%, at least 100%, at least 110%, at least120% more lipid than a control microorganism while producing at least65%, 70%, 75%, 880%, 85%, 90%, 95%, 98%, or 99% of the biomass producedby the control microorganism, under conditions where both the mutantmicroorganism and the control microorganism are producing biomass on adaily basis. The microorganism can in some examples be an alga, and theculture can be a photoautotrophic culture. Culturing can be in batch,semi-continuous, or continuous mode.

The lipid producing microorganisms may be cultured in any suitablevessel(s), including flasks or bioreactors, where the algae may beexposed to artificial or natural light (or natural light supplementedwith artificial light). The culture comprising mutant algae that arederegulated in their response to low light may be cultured on alight/dark cycle that may be, for example, a natural or programmedlight/dark cycle, and as illustrative examples, may provide twelve hoursof light to twelve hours of darkness, fourteen hours of light to tenhours of darkness, sixteen hours of light to eight hours of darkness,etc.

Culturing refers to the intentional fostering of growth (e.g., increasesin cell size, cellular contents, and/or cellular activity) and/orpropagation (e.g., increases in cell numbers via mitosis) of one or morecells by use of selected and/or controlled conditions. The combinationof both growth and propagation may be termed proliferation. Amicroorganism as provided herein may be cultured for at least five, atleast six, at least seven at least eight, at least nine, at least ten,at least eleven at least twelve, at least thirteen, at least fourteen,or at least fifteen days, or at least one, two three, four, five, six,seven, eight, nine, or ten weeks, or longer.

Non-limiting examples of selected and/or controlled conditions that canbe used for culturing the recombinant microorganism can include the useof a defined medium (with known characteristics such as pH, ionicstrength, and/or carbon source), specified temperature, oxygen tension,carbon dioxide levels, growth in a bioreactor, or the like, orcombinations thereof. In some embodiments, the microorganism or hostcell can be grown mixotrophically, using both light and a reduced carbonsource. Alternatively, the microorganism or host cell can be culturedphototrophically. When growing phototrophically, the algal strain canadvantageously use light as an energy source. An inorganic carbonsource, such as CO₂ or bicarbonate can be used for synthesis ofbiomolecules by the microorganism. “Inorganic carbon”, as used herein,includes carbon-containing compounds or molecules that cannot be used asa sustainable energy source by an organism. Typically “inorganic carbon”can be in the form of CO₂ (carbon dioxide), carbonic acid, bicarbonatesalts, carbonate salts, hydrogen carbonate salts, or the like, orcombinations thereof, which cannot be further oxidized for sustainableenergy nor used as a source of reducing power by organisms. Amicroorganism grown photoautotrophically can be grown on a culturemedium in which inorganic carbon is substantially the sole source ofcarbon. For example, in a culture in which inorganic carbon issubstantially the sole source of carbon, any organic (reduced) carbonmolecule or organic carbon compound that may be provided in the culturemedium either cannot be taken up and/or metabolized by the cell forenergy and/or is not present in an amount sufficient to providesustainable energy for the growth and proliferation of the cell culture.

Microorganisms and host cells that can be useful in accordance with themethods of the present invention can be found in various locations andenvironments throughout the world. The particular growth medium foroptimal propagation and generation of lipid and/or other products canvary and may be optimized to promote growth, propagation, or productionof a product such as a lipid, protein, pigment, antioxidant, etc. Insome cases, certain strains of microorganisms may be unable to grow in aparticular growth medium because of the presence of some inhibitorycomponent or the absence of some essential nutritional requirement ofthe particular strain of microorganism or host cell.

Solid and liquid growth media are generally available from a widevariety of sources, as are instructions for the preparation ofparticular media suitable for a wide variety of strains ofmicroorganisms. For example, various fresh water and salt water mediacan include those described in Barsanti (2005) Algae: Anatomy,Biochemistry & Biotechnology, CRC Press for media and methods forculturing algae. Algal media recipes can also be found at the websitesof various algal culture collections, including, as nonlimitingexamples, the UTEX Culture Collection of Algae(www.sbs.utexas.edu/utex/media.aspx); Culture Collection of Algae andProtozoa (www.ccap.ac.uk); and Katedra Botaniky(botany.natur.cuni.cz/algo/caup-media.html).

The culture methods can optionally include inducing expression of one ormore genes and/or regulating a metabolic pathway in the microorganism.Inducing expression can include adding a nutrient or compound to theculture, removing one or more components from the culture medium,increasing or decreasing light and/or temperature, and/or othermanipulations that promote expression of the gene of interest. Suchmanipulations can largely depend on the nature of the (heterologous)promoter operably linked to the gene of interest.

In some embodiments of the present invention, the microorganisms havingincreased lipid productivity can be cultured in a “photobioreactor”equipped with an artificial light source, and/or having one or morewalls that is transparent enough to light, including sunlight, toenable, facilitate, and/or maintain acceptable microorganism growth andproliferation. For production of fatty acid products or triglycerides,photosynthetic microorganisms or host cells can additionally oralternately be cultured in shake flasks, test tubes, vials, microtiterdishes, petri dishes, or the like, or combinations thereof.

Additionally or alternately, mutant or recombinant photosyntheticmicroorganisms or host cells may be grown in ponds, canals, sea-basedgrowth containers, trenches, raceways, channels, or the like, orcombinations thereof. In such systems, the temperature may beunregulated, or various heating or cooling method or devices may beemployed As with standard bioreactors, a source of inorganic carbon(such as, but not limited to, CO₂, bicarbonate, carbonate salts, and thelike), including, but not limited to, air, CO₂-enriched air, flue gas,or the like, or combinations thereof, can be supplied to the culture.When supplying flue gas and/or other sources of inorganic that maycontain CO in addition to CO₂, it may be necessary to pre-treat suchsources such that the CO level introduced into the (photo)bioreactor donot constitute a dangerous and/or lethal dose with respect to thegrowth, proliferation, and/or survival of the microorganisms.

The mutant microorganisms can include one or more non-native genesencoding a polypeptide for the production of a product, such as but notlimited to a lipid.

The methods include culturing a mutant microorganism as provided herein,such as a mutant microorganism as provided herein that has increasedlipid productivity with respect to a control cell while producing atleast 50% of the biomass produced by a control cell under the sameculture conditions to produce biomass or lipid. Lipids can be recoveredfrom culture by recovery means known to those of ordinary skill in theart, such as by whole culture extraction, for example, using organicsolvents or by first isolating biomass from which lipids are extracted(see, for example, Hussein et al. Appl. Biochem. Biotechnol.175:3048-3057; Grima et al. (2003) Biotechnol. Advances 20:491-515). Insome cases, recovery of fatty acid products can be enhanced byhomogenization of the cells (Gunerken et al. (2015) Biotechnol. Advances33:243-260). For example, lipids such as fatty acids, fatty acidderivatives, and/or triglycerides can be isolated from algae byextraction of the algae with a solvent at elevated temperature and/orpressure, as described in the co-pending, commonly-assigned U.S. patentapplication Ser. No. 13/407,817 entitled “Solvent Extraction of Productsfrom Algae”, filed on Feb. 29, 2012, which is incorporated herein byreference in its entirety.

Biomass can be harvested, for example, by centrifugation or filtering.The biomass may be dried and/or frozen. Further products may be isolatedfrom biomass, such as, for example, various lipids or one or moreproteins. Also included in the invention is an algal biomass comprisingbiomass of lipid regulator mutant, such as any disclosed herein, such asbut not limited to a lipid regulator mutant that includes a mutation ina gene encoding a polypeptide having at least 50%, at least 55%, atleast 60%, at least 65%, at least 70%, at least 75%, at least 80%, atleast 85%, at least 90%, or at least 95% identity to a polypeptidecomprising an amino acid sequence selected from the group consisting ofSEQ ID NO:2 and SEQ ID NOs:5-17.

Additional Embodiments

Alternatively or in addition to any of the forgoing embodiments, theinvention provides the following embodiments:

Embodiment 1 is a mutant microorganism that produces at least 25% morelipid and at least 45% more biomass than is produced by a controlmicroorganism cultured under substantially identical conditions in whichthe control microorganism produces biomass, optionally wherein any oneor more of the following are fulfilled:

-   -   (a) the control microorganism is a wild type microorganism;    -   (b) the mutant microorganism produces at least 45%, at least        50%, at least 55%, at least 60%, at least 65%, at least 70%, at        least 75%, at least 80%, at least 85%, at least 90%, at least        95%, at least 100%, as much biomass, which can be assessed as        average biomass (e.g., TOC) productivity per day, during a        culture period of at least three, at least four, at least five,        at least six, at least seven, at least eight, at least nine, at        least ten, at least eleven, at least twelve, at least thirteen        days, at least fourteen, at least fifteen, at least twenty, at        least thirty, or at least sixty days;    -   (c) the mutant microorganism produces at least 25%, at least        30%, at least 55%, at least 40%, at least 45%, at least 50%, at        least 55%, at least 60%, at least 70%, at least 75%, at least        80%, at least 85%, at least 90%, at least 95%, at least 100%, at        least 110%, at least 115%, at least 120%, at least 150% more        lipid, or at least 200% more lipid, which can be assessed as        average lipid (e.g., FAME) productivity per day, than is        produced by a control microorganism during a culture period of        at least at least three, at least four, at least five, at least        six, at least seven, at least eight, at least nine, at least        ten, at least eleven, at least twelve, at least thirteen days,        at least fourteen, at least fifteen, at least twenty, at least        thirty, or at least sixty days;    -   (d) the substantially identical conditions in which the control        microorganism produces biomass comprise a culture medium that        comprises less than about 5 mM, less than about 4 mM, less than        about 3 mM, less than 2.5 mM ammonium, less than 2 mM ammonium,        less than 1.5 mM ammonium, less than or equal to about 1 mM        ammonium, or less than or equal to about 0.5 mM ammonium;    -   (e) the substantially identical conditions in which the control        microorganism produces biomass comprise a culture medium that        comprises nitrate or urea; and/or    -   (f) the microorganism is a heterokont or alga.

Embodiment 2 is a mutant microorganism according to embodiment 1 inwhich the mutant has attenuated expression of a regulator gene whereinthe regulator gene encodes a polypeptide having at least 50, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% to SEQ ID NO:2, SEQ ID NO:5, SEQ IDNO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11,SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16,SEQ ID NO:17, or SEQ ID NO:18 and/or regulator gene encodes apolypeptide that includes a Zn(2)Cys(6) domain, optionally wherein thepolypeptide further includes a PAS3 domain.

Embodiment 3 is a mutant microorganism according to embodiment 1 orembodiment 2, wherein the mutant is a spontaneous mutant, aclassically-derived mutant, or an engineered mutant, optionally whereinthe mutant is an engineered mutants that:

-   -   (a) has a disrupted gene, optionally wherein the gene is        disrupted in a noncoding region;    -   (b) is deleted in all or a portion of a gene;    -   (c) includes an antisense construct, an RNAi construct, or a        ribozyme construct that targets a gene;    -   (d) includes an insertion, optionally wherein the insertion is        generated by CRISPR/cas genome editing; and/or    -   (e) includes a mutation generated by CRISPR/cas genome editing.

Embodiment 4 is a mutant microorganism according to any of embodiments1-3, wherein:

-   -   (a) the mutant produces at least 50% or at least 80% or at least        100% more FAME (e.g., average productivity per day) while        producing at least 85% or at least 90% or at least 95% of the        TOC produced by a control cell, e.g., TOC productivity on a per        day basis, when cultured under conditions in which both the        control and mutant microorganism produce biomass; and/or    -   (b) wherein the FAME/TOC ratio of the mutant microorganism is at        least 40%, at least 50%, at least 60%, at least 70%, or at least        75% higher than the FAME/TOC of the control microorganism while        producing at least 85% or at least 90% of the TOC produced by a        control cell (such as a wild type cell) when cultured under        conditions in which both the control and mutant microorganism        produce biomass; and/or    -   (c) the FAME/TOC ratio of the mutant microorganism is at least        0.30, at least 0.35 at least 0.40, at least 0.5, or between        about 0.3 and about 0.8 when cultured under conditions in which        both the control and mutant microorganism produce biomass and/or    -   (d) wherein the FAME/TOC ratio is maintained between about 0.3        and about 0.7 for a culture period of at least five, at least        six, at least seven, at least eight, at least nine, at least        ten, at least eleven, at least twelve, or at least thirteen days        during which the mutant microorganism produces at least 50%, at        least 60%, at least 70%, or at least 75%, at least 80% or at        least 85% of the biomass produced by a control microorganism        cultured under the same conditions in which the control        microorganism accumulates biomass.

Embodiment 6 is a mutant microorganism according to any of embodiments1-3, wherein:

-   -   (a) the mutant produces at least 85%, at least 90%, at least        95%, at least 100%, at least 105%, at least 110%, or at least        115% more FAME (e.g., on an average per day basis) while        producing at least 70%, at least 75%, at least 80%, or at least        85% of the TOC produced (e.g., on an average per day basis) by a        control microorganism (such as a wild type cell) when cultured        under conditions in which both wild type and mutant        microorganism are producing biomass; and/or    -   (b) the FAME/TOC ratio of the mutant microorganism is at least        100%, at least 110%, at least 120%, at least 130%, at least        140%, at least 150%, at least 160%, at least 170%, or at least        180% greater than the FAME/TOC ratio of a control microorganism        when cultured under conditions in which both wild type and        mutant microorganism are producing biomass; and/or    -   (c) the FAME/TOC ratio of the mutant microorganism is at least        0.50, at least 0.55, at least 0.60, at least 0.65, at least        0.70, or at least 0.75 and the mutant microorganism produces at        least 70%, at least 75%, at least 80%, or at least 85% of the        TOC produced by a control microorganism when cultured under        conditions in which the wild type accumulates biomass.

Embodiment 7 is a mutant microorganism according to any of embodiments1-6, wherein:

-   -   (a) the culture conditions under which the mutant microorganism        produces more lipid is batch, semi-continuous, or continuous        culture; and/or    -   (b) the daily lipid productivity of the mutant is greater than        the daily lipid productivity of the control microorganism        throughout the culture period.

Embodiment 8 is a mutant microorganism according to any of embodiments1-7 in which the mutant microorganism comprises a mutation in anon-coding region of a gene that reduces expression of the gene,optionally wherein the mutation is an insertion.

Embodiment 9 is a mutant microorganism according to any of embodiments1-7 in which the mutant microorganism comprises a construct that reducesexpression of a gene, wherein the construct encodes an RNAi, antisensetranscript, or ribozyme.

Embodiment 10 is a mutant microorganism according to any of embodiments1-9, wherein the mutant microorganism is a Labyrinthulomycte species,

-   -   (a) optionally wherein the mutant microorganism is a species        belonging to any of the genera Labryinthula, Labryinthuloides,        Thraustochytrium, Schizochytrium, Aplanochytrium,        Aurantiochytrium, Oblongichytrium, Japonochytrium, Diplophrys,        or Ulkenia; or

wherein the mutant microorganism is an algal species,

-   -   (b) optionally a species belonging to any of the genera        Achnanthes, Amphiprora, Amphora, Ankistrodesmus, Asteromonas,        Boekelovia, Bolidomonas, Borodinella, Botrydium, Botryococcus,        Bracteococcus, Chaetoceros, Carteria, Chlamydomonas,        Chlorococcum, Chlorogonium, Chlorella, Chroomonas,        Chrysosphaera, Cricosphaera, Crypthecodinium, Cryptomonas,        Cyclotella, Desmodesmus, Dunaliella, Elipsoidon, Emiliania,        Eremosphaera, Ernodesmius, Euglena, Eustigmatos, Franceia,        Fragilaria, Fragilaropsis, Gloeothamnion, Haematococcus,        Hantzschia, Heterosigma, Hymenomonas, Isochrysis, Lepocinclis,        Micractinium, Monodus, Monoraphidium, Nannochloris,        Nannochloropsis, Navicula, Neochloris, Nephrochloris,        Nephroselmis, Nitzschia, Ochromonas, Oedogonium, Oocystis,        Ostreococcus, Parachlorella, Parietochloris, Pascheria, Pavlova,        Pelagomonas, Phceodactylum, Phagus, Picochlorum, Platymonas,        Pleurochrysis, Pleurococcus, Prototheca, Pseudochlorella,        Pseudoneochloris, Pseudostaurastrum, Pyramimonas, Pyrobotrys,        Scenedesmus, Schizochlamydella, Skeletonema, Spyrogyra,        Stichococcus, Tetrachlorella, Tetraselmis, Thalassiosira,        Tribonema, Vaucheria, Viridiella, Vischeria, and Volvox.

Embodiment 11 is biomass comprising any of the mutant microorganisms ofany of embodiments 1-10.

Embodiment 12 is a nucleic acid molecule comprising a sequence encodinga polypeptide having at least 60%, at least 65%, at least 70%, or atleast 75%, at least 80%, at least 85%, at least 90%, or at least 95%identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ IDNO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ IDNO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17;

-   -   wherein any one or more of the following are satisfied:        -   (a) the polypeptide includes an amino acid sequence encoding            a Zn(2)Cys(6) domain, optionally wherein the Zn(2)Cys(6)            domain has at least 60%, at least 65%, at least 70%, or at            least 75%, at least 80%, at least 85%, at least 90%, or at            least 95% identity to SEQ ID NO:3;    -   the polypeptide includes an amino acid sequence encoding a PAS        domain, optionally wherein the PAS domain has at least 60%, at        least 65%, at least 70%, or at least 75%, at least 80%, at least        85%, at least 90%, or at least 95% identity to any of SEQ ID        NO:21-SEQ ID NO:25;        -   (b) the nucleic acid molecule in various examples comprises            a cDNA that lacks one or more introns present in the            naturally-occurring gene or is a gene construct that            includes one or more introns not present in the            naturally-occurring gene;        -   (c) the nucleic acid molecule in various examples can have a            sequence that is not 100% identical to a naturally-occurring            gene;        -   (d) the nucleic acid molecule has at least 50%, at least            55%, at least 60%, at least 65%, at least 70%, or at least            75%, at least 80%, at least 85%, at least 90%, or at least            95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ            ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID            NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID            NO:15, SEQ ID NO:16, or SEQ ID NO:17;        -   (e) the nucleic acid molecule comprises a heterologous            promoter operably linked to the sequence; and/or        -   (f) the nucleic acid molecule comprises a vector.

Embodiment 13 is a nucleic acid molecule construct for attenuatingexpression of a gene encoding a polypeptide according to having at least60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5,SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ IDNO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ IDNO:16, or SEQ ID NO:17;

-   -   a sequence encoding a guide RNA of a CRISPR system, an RNAi        construct, an antisense construct, a ribozyme construct, or a        construct for homologous recombination, e.g., a construct having        one or more nucleotide sequences having homology to a        naturally-occurring Zn(2)Cys(6) domain-encoding gene as        disclosed herein and/or sequences adjacent thereto in the native        genome from which the gene is derived.

Embodiment 14 is method of engineering a cell for increased lipidproduction comprising attenuating expression of a gene encoding apolypeptide having at least 60%, at least 65%, at least 70%, or at least75%, at least 80%, at least 85%, at least 90%, or at least 95% identityto SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ IDNO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17, optionally a geneencoding a polypeptide having an amino acid sequence having at least55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least80%, at least 85%, at least 90%, or at least 95% identity to any of SEQID NOs:21-25, into a microorganism to produce a mutant microorganismhaving higher lipid productivity than the progenitor microorganism,optionally wherein attenuating expression of the gene comprisesintroducing a nucleic acid molecule according to embodiment 13 into themicroorganism.

Embodiment 15 is method for producing lipid comprising culturing amutant according to any of embodiments 1-10 to produce lipid, optionallywherein any one or more of the following are satisfied:

-   -   (a) the culture medium includes nitrate or urea;    -   (b) the culture medium includes less than 5 mM, less than 4 mM,        less than 3 mM, less than 2.5 mM ammonium, less than 2 mM        ammonium, less than or equal to about 1.5 mM ammonium, less than        or equal to about 1 mM ammonium, or less than or equal to about        0.5 mM ammonium;    -   (c) the culture is a batch, semi-continuous, or continuous        culture;    -   (d) the culture period is at least 5, 7, 8, 9, 10, 11, 12, 13        day, at least 15, 20, 30, 40, 50, or 60 days;    -   (e) the mutant is an algal mutant and the culture is        photoautotrophic;    -   (f) the mutant produces at least 25% more lipid, such as at        least 50% more lipid, preferably FAME lipid, and at least 65% of        the biomass of a control microorganism during the culture        period;    -   (g) the mutant produces more lipid, preferably FAME lipid, on        each day of the culture period; and/or    -   (h) the mutant accumulates biomass on each day of the culture        period.

Embodiment 16 is method for producing lipid comprising culturing amicroorganism under conditions in which the FAME/TOC ratio is maintainedat between about 0.3 and about 0.8 throughout the culture period,optionally wherein any one or more of the following are satisfied:

-   -   (a) the culture medium includes nitrate or urea;    -   (b) the culture medium includes less than 5 mM, less than 4 mM,        less than 3 mM, less than 2.5 mM ammonium, less than 2 mM        ammonium, less than or equal to about 1.5 mM ammonium, less than        or equal to about 1 mM ammonium, or less than or equal to about        0.5 mM ammonium;    -   (c) the culture is a batch, semi-continuous, or continuous        culture;    -   (d) the culture period is at least 5, 7, 8, 9, 10, 11, 12, 13        day, at least 15, 20, 30, 40, 50, or 60 days;    -   (e) the microorganism is an algal microorganism and the culture        is photoautotrophic;    -   (f) the microorganism accumulates biomass on each day of the        culture period; and/or    -   (g) the microorganism is a mutant microorganism according to any        of embodiments 1-1

EXAMPLES Media Used in Examples

The following media are used in the Examples.

PM066 medium (Example 1) includes 8.8 mM nitrate as the sole nitrogensource. PM066 medium included 10 mM nitrate (NO₃) and 0.417 mM phosphate(PO₄) along with trace metals and vitamins in Instant Ocean salts. PM066media was made by adding 5.71 ml of a 1.75 M NaNO₃ stock solution (148.7g/L), and 5.41 ml of a 77 mM K₂HPO₄.3H₂O stock solution (17.57 g/L) to981 mls of Instant Ocean salts solution (35 g/L) along with 4 ml ofChelated Metals Stock Solution and ml of 4 ml Vitamin Stock Solution.Chelated Metals Stock Solution was prepared by adding to 400 mls ofwater 2.18 g Na₂EDTA.2H₂O; 1.575 g FeCl₃.6H₂O; 500 μl of 39.2 mM stocksolution (0.98 g/100 ml) CuSO₄.5H₂O; 500 μl of 77.5 mM stock solution(2.23 g/100 ml) ZnSO₄.7H₂O; 500 μl of 42.0 mM stock solution (1.00 g/100ml) CoCl₂.6H₂O; 500 μl of 910.0 mM stock solution (18.0/100 ml)MnCl₂.4H₂O; 500 μl of 26.0 mM stock solution (0.63 g/100 ml)Na₂MoO₄.2H₂O; bringing up to 500 ml final volume, and filtersterilizing. Vitamin Stock Solution was prepared by adding to 400 mls ofwater 0.05 g Thiamine HCl; 500 μl of 0.37 mM stock solution (0.05 g/100ml) of cyanocobalamin; and 2.5 ml of 0.41 mM stock solution (0.01 g/100ml) of biotin, bringing up to a final volume of 500 mls, and filtersterilizing.

PM067 medium included no nitrogen source (no nitrate, ammonium, orurea), and 0.417 mM phosphate (PO₄) along with trace metals and vitaminsin Instant Ocean salts. PM067 media was made by adding 5.41 ml of a 77mM K₂HPO₄.3H₂O stock solution (17.57 g/L) to 987 mls of Instant Oceansalts solution (35 g/L) along with 4 ml of Chelated Metals StockSolution and ml of 4 ml Vitamin Stock Solution. Chelated Metals StockSolution was prepared by adding to 400 mls of water 2.18 g Na₂EDTA.2H₂O;1.575 g FeCl₃.6H₂O; 500 μl of 39.2 mM stock solution (0.98 g/100 ml)CuSO₄.5H₂O; 500 μl of 77.5 mM stock solution (2.23 g/100 ml) ZnSO₄.7H₂O;500 μl of 42.0 mM stock solution (1.00 g/100 ml) CoCl₂.6H₂O; 500 μl of910.0 mM stock solution (18.0/100 ml) MnCl₂.4H₂O; 500 μl of 26.0 mMstock solution (0.63 g/100 ml) Na₂MoO₄.2H₂O; bringing up to 500 ml finalvolume, and filter sterilizing. Vitamin Stock Solution was prepared byadding to 400 mis of water 0.05 g Thiamine HCl; 500 μl of 0.37 mM stocksolution (0.05 g/100 ml) of cyanocobalamin; and 2.5 ml of 0.41 mM stocksolution (0.01 g/100 ml) of biotin, bringing up to a final volume of 500mis, and filter sterilizing.

PM074 is a nitrogen replete (“nitrate-only”) medium (includes nitrate assubstantially the sole nitrogen source) that is 10×F/2 made by adding1.3 ml PROLINE® F/2 Algae Feed Part A (Aquatic Eco-Systems) and 1.3 mlPROLINE® F/2 Algae Feed Part B (Aquatic Eco-Systems) to a final volumeof 1 liter of a solution of Instant Ocean salts (35 g/L) (Aquatic EcoSystems, Apopka, Fla.). Proline A and Proline B together include 8.8 mMNaNO₃, 0.361 mM NaH₂PO₄.H₂O, 10×F/2 Trace metals, and 10×F/2 Vitamins(Vuillard (1975) Culture of phytoplankton for feeding marineinvertebrates in “Culture of Marine Invertebrate Animals.” (eds: SmithW. L. and Chanley M. H.) Plenum Press, New York, USA. pp 26-60).

PM123 medium is PM074 medium supplemented with additional Proline B sothat the concentration of nitrate was increased from approximately 8.8mM to approximately 15 mM. This is also a “nitrate only” medium.

PM124 medium is PM074 supplemented with 5 mM ammonium and 10 mM HEPES pH8.0. It is made by adding 10 mis of 1 M HEPES pH 8 and 5 mis of NH₄Cl tothe PM074 recipe (final volume of 1 L). In some examples, additionalmedia with controlled ammonium levels was made by adjusting the ammoniumconcentration of PM074 and adding additional Hepes buffer.

PM125 medium (Example 5): includes 7.5 mM urea as the only source ofnitrogen available to the cells. To 1× instant ocean was added (whilemixing): 3.75 ml 2M Urea stock solution, 0.32 ml 1 M NaH₂PO₄ stocksolution, 4 ml of Chelated Metals Stock Solution and ml of 4 ml VitaminStock Solution (see above). The media was filter sterilized through <0.1μm filter and stored at room temperature.

Example 1 Identification of a Zinc-Cys Domain Polypeptide Down-RegulatedDuring Nitrogen Starvation

Various strains of Nannochloropsis accumulate high levels oftriacylglycerols (TAG) storage lipid during nitrogen deprivation andcorrelations between increased TAG production and correlations betweenTAG accumulation and presumed underlying changes in gene expression indifferent metabolic pathways leading to TAG synthesis have been reported(Radakovits et al. (2012) Nat Commun 3: 686; Li et al. (2014) The PlantCell 26: 1645-1665; Corteggiani Carpinelli et al. (2014) Mol Plant7:1645-1665). To identify genes encoding regulators that influence lipidbiosynthesis and accumulation, the early transcriptional response ofNannochloropsis cells subjected to N-deprivation (−N) was analyzed. Acomparative transcriptomics experiment was performed in which the RNAtranscript levels of genes of Nannochloropsis gaditana cells undernitrogen starvation, during which Nannochloropsis induces storage lipidbiosynthesis, were compared with the levels of RNA transcripts of thesame strain of Nannochloropsis gaditana grown under identical conditionsexcept that the amount of nitrogen in the growth medium was notlimiting.

Wild type N. gaditana (WT-3730) cells were grown in nutrient repletemedium under a 16 hour light (120 μE)/8 hour dark cycle to lightlimitation (to O.D. of 1.25) and at the beginning of the photoperiodwere spun down and resuspended in either nitrogen replete medium PM066or culture medium lacking a nitrogen source (“nitrogen deplete” or “—N”medium PM067) and incubated under the provided light conditions. RNA wasisolated from samples removed at various time intervals afterresuspension of the cells in nitrogen replete (+N) or nitrogen deplete(−N) medium. Lipid accumulation was determined from samples takenthroughout the assay. Lipid accumulation (measured as FAME as describedin Example 4) was indistinguishable between nitrogen deplete andnitrogen replete cultures at the 3 h timepoint, but at 10 h FAMEaccumulation in the nitrogen deplete culture was double that of thenitrogen replete culture (FIG. 1A). Treatments were performed inbiological triplicates. Under the assumption that transcriptionalchanges should precede metabolic changes, the 3 h time-point wasselected for mRNA sequencing. Two samples for each treatment weresequenced.

RNA was isolated by spinning down 10 mLs of each algal cell culture(4000×g for 5 minutes) and decanting the supernatant. The pellets wereresuspended in 1.8 mL Buffer A (5 mL TLE Grinding Buffer, 5 mL phenol, 1mL 1-bromo-3-chloropropane and 20 μL mercaptoethanol, where TLE GrindingBuffer includes 9 mL of 1M Tris pH 8, 5 mL of 10% SDS, 0.6 mL of 7.5 MLiCl, and 450 μl 0.5 M EDTA in a final volume of 50 mL) and transferredto 2 mL microcentrifuge tubes containing approximately 0.5 mL of 200 μmzirconium beads. The tubes were vortexed vigorously for 5 min at 4° C.and then centrifuged for 2 min at 11.8×g. The aqueous layers were thenremoved and pipetted into new 2 mL tubes, to which 1 mL 25:24:1 phenolextraction buffer (25 mL phenol pH 8.1; 24 mL 1-bromo-3-chloropropane,and 1 mL isoamyl alcohol) was added. The tubes were shaken vigorouslyand centrifuged for 2 min at 11.8×g. After centrifugation, the aqueouslayer was removed and pipetted into new 2 mL centrifuge tubes, to which1 ml 1-bromo-3-chloropropane was added. The tubes were shaken and againcentrifuged for 2 min at 11.8×g. The aqueous layer was removed to a newtube and 0.356 volumes of 7.5 M LiCl were added. The tubes were inverted10-12 times and stored at −20° C. overnight. The next day, samples wereallowed to come to room temperature without mixing and were centrifugedat 16,000×g for 30 minutes. The supernatants were removed and thepellets were washed with 1 mL of ice cold 80% ethanol. The tubes werecentrifuged for 30 min at 16,000×g and allowed to air dry after thesupernatants had been removed. Finally, the RNA pellets were resuspendedin 50 μl ultrapure water. The RNA quality was assessed by on-chip gelelectrophoresis using an Agilent 2100 Bioanalyzer and RNA6000 LabChipaccording to manufacturer instructions.

Next-generation sequencing libraries were prepared from the isolated RNAutilizing the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego,Calif.) following manufacturer instructions. The TruSeq libraries weresequenced using sequencing-by-synthesis (Illumina MiSeq) to generate 100bp paired-end reads using the mRNA-Seq procedure (described in Mortazaviet al. (2008) Nature Methods 5:621-628). Mappable reads were aligned tothe N. gaditana reference genome sequence using TopHat(tophat.cbcb.umd.edu/). Expression levels were computed for everyannotated gene using the Cuffdiff component of the Cufflinks software(cufflinks.cbcb.umd.edu). TopHat and Cufflinks are described in Trapnellet al. (2012) Nature Protocols 7: 562-578. Differential expressionanalysis was performed using the R package edgeR (McCarthy et al. (2012)Nucl. Acids Res. 40:doi:10/1093/nar/gks042)). Expression levels in unitsof fragments per kilobase per million (FPKM) were reported for everygene in each sample using standard parameters. FPKM is a measure ofrelative transcriptional levels that normalizes for differences intranscript length.

Global analysis of the transcriptome of −N and +N cultures at 3 hrevealed 1064 differentially expressed genes having a difference inexpression of greater than 1 fold and a false discovery rate (FDR) ofless than 0.01. These genes are depicted as dots and Xs in the plot ofFIG. 1B. Of these genes, 363 were upregulated (right side of the plot)and 701 were down-regulated in the —N condition (left side of the plot).The list of differentially expressed genes was compared with abioinformatically curated list of putative Nannochloropsis transcriptionfactors previously generated by mining the Nannochloropsis genome forproteins containing DNA binding domains and other conserved pfam domainstypical of characterized transcription factors using the PlantTranscription Factor Database as a reference (Perez-Rodriguez et al.(2010) Nucl. Acids Res. 38: D822-D827; Jin et al. (2013) Nucl. AcidsRes. 42: D1182-D1187). We found 20 transcription factors, represented asXs in FIG. 1B and listed in Table 1, that were represented only in thedown-regulated set of transcription factors. No transcription factorswere found to be upregulated at the 3 h timepoint. N. gaditana geneidentifiers are based on the genome sequence described in CorteggianiCarpinelli et al., Mol Plant 7, 323-335 (2014).

TABLE 1 Transcription Factors Targeted for Knockout by Cas9 PCR PositiveFold Lines/ Change Lines N. gaditana id Gene Description (log 2) FDR^(†)Screened Success^(††) Naga_100055g29 CCT domain protein −3.3 5.4E−1513/31 Y Naga_100104g18 Zn(2)-C6 fungal-type DNA- −2.5 1.5E−19 19/29 Ybinding domain protein Naga_100043g41 RpoD family RNA polymerase −1.65.3E−10  0/31 N sigma factor SigA Naga_100146g3 Fungal Zn(2)-Cys(6)binuclear −1.6 1.7E−02 24/31 Y cluster domain Naga_101321g2 Zinc finger,CCCH-type −1.5 4.5E−03  9/30 Y Naga_100489g1 Zinc finger, TAZ-type −1.43.6E−05 1/6 Y Naga_100042g29 SANT/Myb domain protein −1.4 1.1E−03 17/32Y Naga_100248g8 Winged helix-turn-helix −1.3 3.1E−04  3/23 Ytranscription repressor DNA-binding Naga_100066g21 CCT motif familyprotein −1.3 9.6E−06  5/30 Y Naga_100084g18 Myb-like DNA-binding shaqkyf−1.2 8.6E−06 17/32 Y class family protein Naga_100339g1 Nucleicacid-binding protein −1.2 1.6E−04 0/8 N Naga_100087g2 Activatingtranscription factor 6 −1.1 9.0E−05 16/29 Y Naga_100249g5 FungalZn(2)-Cys(6) binuclear −1.1 4.1E−06 19/31 Y cluster domain Naga_100329g4Fungal specific transcription factor −1.1 9.1E−04 14/31 Ydomain-containing region Naga_100028g52 Zn(2)-C6 fungal-typetranscription −0.9 2.5E−03 10/31 Y factor Naga_100019g66 Wingedhelix-turn-helix −0.9 1.1E−03 22/31 Y transcription repressorNaga_100146g5 Fungal Zn(2)-Cys(6) binuclear −0.9 9.9E−04 14/31 Y clusterdomain Naga_100086g13 Myb-like dna-binding domain −0.9 7.7E−04 25/32 Ycontaining protein Naga_100001g82 Fungal Zn(2)-Cys(6) binuclear −0.93.6E−03  2/32 Y cluster domain Naga_100001g77 Aureochrome1-like protein−0.5 3.9E−02 16/32 Y ^(†)FDR, False discovery rate ^(††)Y, successfulinsertion of the selection cassette;N, unsuccessful insertion, as determined by PCR genotyping

Example 2 Knockout of Transcription Factor Genes in Nannochloropsis

All 20 transcription factor genes that were discovered to bedifferentially regulated under nitrogen deprivation (Table 1) weretargeted for insertional knockout mutagenesis via the development of ahigh-efficiency Cas9-expressing editor line in Nannochloropsis (see WO2016/109840 and corresponding U.S. application Ser. No. 14/986,492,filed Dec. 31, 2015, incorporated herein by reference in its entirety).As described in U.S. Ser. No. 14/986,492, a highly efficientNannochloropsis Cas9 Editor line, N. gaditana strain GE-6791, expressinga gene encoding the Streptococcus pyogenes Cas9 nuclease, was used as ahost for transformation with a chimeric guide RNA and donor DNA forinsertional knockout.

To produce the high efficiency Nannochloropsis Cas9 Editor line, aNannochloropsis strain was engineered and isolated that exhibitedexpression of the introduced cas9 gene in essentially 100% of the cellpopulation of a growing culture. The vector pSGE-6206 (FIG. 2; SEQ IDNO:26), used to transform wild type N. gaditana strain WT-3730 includedthe following three elements: 1) a Cas9 expression cassette whichcontained a Cas9 gene from Streptococcus pyogenes codon optimized forNannochloropsis gaditana (SEQ ID NO:27) that also included sequencesencoding an N-terminal FLAG tag (SEQ ID NO:28), nuclear localizationsignal (SEQ ID NO:29), and peptide linker (entire FLAG, NLS, and linkersequence provided as SEQ ID NO:30), driven by the N. gaditana RPL24promoter (SEQ ID NO:31) and terminated by N. gaditana bidirectionalterminator 2 or “FRD” terminator (SEQ ID NO:32); 2) a selectable markerexpression cassette, which contained the blasticidin deaminase (“blast”or “BSD”) gene from Aspergillus terreus codon optimized for N. gaditana(SEQ ID NO:33), driven by the N. gaditana TCTP promoter (SEQ ID NO:34)and followed by the EIF3 terminator (SEQ ID NO:35); and 3) a GFPreporter expression cassette, which contained the TurboGFP gene(Evrogen, Moscow, Russia) codon optimized for Nannochloropsis gaditana(SEQ ID NO:36), driven by the N. gaditana 4A-III promoter (SEQ ID NO:37)and followed by the N. gaditana bidirectional terminator 5 or “GNPDA”terminator (SEQ ID NO:38). The Cas9 expression construct was assembledaccording to the Gibson Assembly® HiFi 1 Step Kit (Synthetic Genomics,La Jolla, Calif.) into a minimal pUC vector backbone; the confirmed DNAsequence of this plasmid is provided as SEQ ID NO:26.

The ZraI-linearized Cas9 expression construct (FIG. 3A) was transformedinto Nannochloropsis cells by electroporation. 1×10⁹ cells weretransformed in a 0.2 cm cuvette using a field strength of 7,000 V/cmdelivered with the Gene Pulser II (Biorad, Carlsbad, Calif., USA). Thetransformation mixture was plated onto PM074 agar medium containing 100mg/L of blasticidin. Resulting colonies were patched onto selectionmedia for analysis and archiving. A small amount of biomass was takenfrom the patches and completely resuspended in 300 μl of 1× InstantOcean Salts solution (Aquatic Eco Systems; Apopka, Fla.). Care was takento not add too much biomass so that a light green resuspension wasobtained. This suspension was directly analyzed by flow cytometry usinga BD Accuri C6 flow cytometer, using a 488 nm laser and 530/10 nm filterto measure GFP fluorescence per cell. 10,000-30,000 events were recordedfor each sample using the slow fluidics setting. A strain having asingle fluorescence peak that was shifted to a fluorescence level higherthan that demonstrated by wild-type cells (FIG. 3B) and alsodemonstrating cas9 protein expression by Western blotting using ananti-FLAG antibody (Sigma #A9469) (FIG. 3C), designated strain GE-6791,was selected as a cas9 Editor strain and used in mutant generation bycas9/CRISPR genome editing as described herein. The Ng-Cas9 Editor linewas found to be equivalent to wild-type in FAME and TOC productivity(see for example FIG. 18).

Generation of Targeted Insertional Mutants in the Ng-Cas9 Editor Line

All 20 identified transcription factors that were found to bedownregulated under nitrogen starvation (Table 1) were targeted forknockout in the Cas9 Editor line. Guide RNAs (see Table 2 for the targetsequences used for knockout of each of the 23 transcription factors)were synthesized in vitro according to (Cho et al. (2013) NatureBiotechnol. 31: 230-232) and described in Example 3, andco-electroporated with a PCR amplified expression cassette (pHygR, SEQID NO:45) containing a codon optimized hygromycin resistance gene (HygR,SEQ ID NO:44) driven by endogenous the EIF3_promoter (SEQ ID NO:46) andfollowed by N. gaditana NADH-dependent fumarate reductase bidirectionalterminator (SEQ ID NO:32) in inverted orientation.

Approximately 1 μg each of the guide RNA targeting the particulartranscription factor and the pHygR donor fragment (FIG. 4A) were addedto the cuvette and electroporation was performed as described above. Ingeneral, loss-of-function “knockout” mutants were generated by selectinga guide RNA target locus in the first half of exonic coding sequence.Selection of HygR transformants was as above except that 500 mg/Lhygromycin was added to agar plates instead of blasticidin. Targetedinsertion of the pHygR fragment via NHEJ-mediated repair of the doublestranded DNA break catalyzed by Cas9 in loci targeted by guide RNAs wasassessed by colony PCR using primers that flanked the guide RNA targetsite by ˜200 bp on either side (Table 3). Using these primers, PCRamplification of wild-type loci would result in ˜400 bp products,whereas pHygR targeted insertional mutants would result in 2800 bpproducts—accounting for the insertion of the 2400 bp pHygR fragment. PCRproducts were sequence-confirmed for all mutants allowing for thedetermination of insert orientation and detection of any loss ofchromosomal and/or insert DNA, or the gain of small insertions generatedduring the NHEJ-mediated dsDNA break repair process (see FIGS. 4B and 4Cfor a diagram of the insertion process and exemplary colony PCRresults).

Eighteen of the 20 targeted transcription factors (Table 1) weredisrupted at the intended locus as confirmed by PCR genotyping. Based onthe high overall editing efficiency observed it is likely that theremaining 2 loci were essential for viability. To test the knockouts foreffects on lipid induction, two independent mutants per locus werescreened for lipid and biomass productivities by assessing FAME and TOClevels throughout multiple time-points of a 7-day culture as describedin detail in Example 4, below.

TABLE 2 Guide RNA Sequences and Screening Primers Used in Cas9-MediatedMutagenesis Target Sequence Adjacent N. gaditana id Descriptionto PAM (NGG) Naga_100055g29 CCT domain protein TTCCGAAGTACTGGTTC(SEQ ID NO: 87) Naga_100104g18 Zn(2)-C6 fungal-type DNA-binding domainAGTAGGCCATTCCCGGAG protein (ZnCys-2845) (SEQ ID NO: 88) Naga_100489g1Zinc finger, TAZ-type TGTGGCAGACGCCGACGG (SEQ ID NO: 89) Naga_100043g41RpoD family RNA polymerase sigma factor SigA GTACTGCCTGACAAACTAGG(SEQ ID NO: 90) Naga_100146g3Fungal Zn(2)-Cys(6) binuclear cluster domain TGAGCAGTCGTACGAAA(SEQ ID NO: 91) Naga_101321g2 Zinc finger, CCCH-type CGAAGTCAACCATGGGGC(SEQ ID NO: 92) Naga_100248g8Winged helix-turn-helix transcription repressor TCCTGTGACTTGACGGTGDNA-binding (SEQ ID NO: 93) Naga_100042g29 SANT/Myb domain proteinGGCAATACAAGCAGTGGAAG (SEQ ID NO: 94) Naga_100066g21CCT motif family protein CTGATCTCGAGATGGCTG (SEQ ID NO: 95)Naga_100329g4 Fungal specific transcription factor domain-GTGAAGATTGGTCCCACT containing protein (SEQ ID NO: 96) Naga_100084g18Myb-like DNA-binding shaqkyf class family GGACGCTACGACCGTGCGGG protein(SEQ ID NO: 97) Naga_100339g1 Nucleic acid-binding proteinCTGCACCAGACACAAATT (SEQ ID NO: 98) Naga_100087g2Activating transcription factor 6 GGGAAATATTAAGACTGGAG (SEQ ID NO: 99)Naga_100249g5 Fungal Zn(2)-Cys(6) binuclear cluster domainTCACGGGAGATGTCCTGT (SEQ ID NO: 100) Naga_100028g52Zn(2)-C6 fungal-type transcription factor AGGACTCTCCTCAGCTGA(SEQ ID NO: 101) Naga_100019g66Winged helix-turn-helix transcription repressor TCTTCATCTGCGACAACG(SEQ ID NO: 102) Naga_100146g5Fungal Zn(2)-Cys(6) binuclear cluster domain ACGTCCGAATATACCGAA(SEQ ID NO: 103) Naga_100086g13Myb-like dna-binding domain containing protein GTAGAACAAGCGTTAGACC(SEQ ID NO: 104) Naga_100001g82Fungal Zn(2)-Cys(6) binuclear cluster domain CGCCACCCTCGCACGTGTC(SEQ ID NO: 105) Naga_100001g77 Aureochromel-like proteinGGCACCATCCCCACCGGTTT (SEQ ID NO: 106) Naga_100104g18ZnCys-2845 (Guide targets 5′UTR resulting in GGGACTGTCCCATTGTGCstrain ZnCys-2845 BASH-3) (SEQ ID NO: 54) Naga_100104g18ZnCys-2845 (Guide targets 3′UTR resulting in AACTCGCTCGTCGATCACstrain ZnCys-2845 BASH-12) (SEQ ID NO: 62) Naga_100699g1Nitrate Reductase GGGTTGGATGGAAAAAGGCA (SEQ ID NO: 193)

TABLE 3 Screening Primers Used in Cas9-Mediated MutagenesisN. gaditana id Genotyping Primer (Sense) Genotyping Primer (Antisense)Naga_100055g29 AAGTGCGCAAGACGCTCCAG TTTGAATATCTGCACATGCA(SEQ ID NO: 107) (SEQ ID NO: 108) Naga_100104g18 ACCTCCTTGTCACTGAGCAGGATCCCAAAGGTCATATCCGT ZnCys-2845 (SEQ ID NO: 109) (SEQ ID NO: 110)Naga_100489g1 ACTCTGTGCTACCAATTGCTG CGTCAGCAAATCTTGCACCA(SEQ ID NO: 111) (SEQ ID NO: 112) Naga_100043g41 GAGATGCTGTCCGAGACACGGTATCTCGGACAGGGCACTG (SEQ ID NO: 113) (SEQ ID NO: 114) Naga_100146g3ATCCATGTAAAGACGATGTGC TGATATCACATGCTCAAGGTC (SEQ ID NO: 115)(SEQ ID NO: 116) Naga_101321g2 AGATGAGGATCAAGCACCGAGCCAGGAAGAAATAGTAGTTGCGTG (SEQ ID NO: 117) (SEQ ID NO: 118) Naga_100248g8AGGCGCTCTGATTGCTGTGGC TCTTCCACGTCGGATGGCCAG (SEQ ID NO: 119)(SEQ ID NO: 120) Naga_100042g29 ATTGTGGAGGGTAACAAACTACGTGAGTCCCGTGGAGAGGAGTCG (SEQ ID NO: 121) (SEQ ID NO: 122) Naga_100066g21AGGTTCCAATGGAGGCCGCA CACTTTCCTTCGTACGCTCAGC (SEQ ID NO: 123)(SEQ ID NO: 124) Naga_100329g4 CTCGAGGTAGGTGGTGAAAG GTGATTCGCATGGACGAAC(SEQ ID NO: 125) (SEQ ID NO: 126) Naga_100084g18 ATGGGTACGGACTTGTTCGACAGCGATACGGACAGTGAC (SEQ ID NO: 127) (SEQ ID NO: 128) Naga_100339g1GACGTTGCATGAGAAAGGAG GATGCACAGGTGCTTGTTAG (SEQ ID NO: 129)(SEQ ID NO: 130) Naga_100087g2 TGCAAAGCCTATTTCCGACG CTCATTCGTGAGGTGACCAT(SEQ ID NO: 131) (SEQ ID NO: 132) Naga_100249g5 GAGCAAACTGACATTGATACGTACCACACATACACATG (SEQ ID NO: 133) (SEQ ID NO: 134) Naga_100028g52CACATCCACCATCATTCCAC GAGTGTTCCCAGTGAGCCAG (SEQ ID NO: 135)(SEQ ID NO: 136) Naga_100019g66 CTGACAAGAAGATGGACATGCTTTAGTTATACGTCTGAAG (SEQ ID NO: 137) (SEQ ID NO: 138) Naga_100146g5GAGAGGATAGTTCTCAGAG GTCCCACAATCTATTGTG (SEQ ID NO: 139) (SEQ ID NO: 140)Naga_100086g13 ATGAGTACTTGCGCGCTTTG GCATGCCTCCGTCACAGAGT(SEQ ID NO: 141) (SEQ ID NO: 142) Naga_100001g82 ATCCATTGAGCATGCCGACGGCAACATGTTAATGCATCGT (SEQ ID NO: 143) (SEQ ID NO: 144) Naga_100001g77TCGTCCTCGAACTCTTCCTC CGGGAACAACCAAGGTGTAA (SEQ ID NO: 145)(SEQ ID NO: 146) Naga_100104g18 TAGCAGAGCAGGCTCATCACGAATATGTGGTCTAGCTCGT ZnCys-2845 (SEQ ID NO: 147) (SEQ ID NO: 148) BASH-3Naga_100104g18 ATGGCTCCACCCTCTGTAAG CTGACTACAGCTAGCACGAT ZnCys-2845(SEQ ID NO: 149) (SEQ ID NO: 150) BASH-12 Naga_100699g1AAGACTTTGGAGGATGTCTGAGTGG ACGAAGCTACATCCAGTGCAAGG (SEQ ID NO: 151)(SEQ ID NO: 152)

Example 3 ZNCYS-2845 Knockout Mutant

The ZnCys-2845 gene (Naga_100104 g18, second row of Table 1) wastargeted for disruption by first making a DNA construct for producing aguide RNA in which the construct included the sequence of a chimericguide engineered downstream of a T7 promoter. The chimeric guidesequence included an 18 bp target sequence (SEQ ID NO:39) homologous toa sequence within the ZnCys-2845 gene sequence that was immediatelyupstream of an S. pyogenes cas9 PAM sequence (NGG), and also includedthe transactivating CRISPR (tracr) sequence. The chimeric guide sequencewas synthesized by first making a DNA template made up of complementaryDNA oligonucleotides that included the T7 promoter sequence (SEQ IDNO:40 and SEQ ID NO:41, made by SGI-DNA, La Jolla, Calif.) thatincorporated the T7 promoter sequence and were annealed to create adouble-stranded DNA template which was used in in vitro transcriptionreactions using the MEGAshortscript™ T7 Kit (Life Technologies #AM1354M)according to the manufacturer's instructions to synthesize the guideRNA. The resulting RNA was purified using Zymo-Spin™ V-E columns (ZymoResearch #C1024-25) according to manufacturer's protocol.

The donor fragment for insertion into the targeted ZnCys-2845 locus (SEQID NO:44) included a selectable marker cassette that included thehygromycin resistance gene (HygR, SEQ ID NO:45) downstream of the N.gaditana EIF3 promoter (SEQ ID NO:46) and followed by N. gaditanabidirectional terminator 2 (SEQ ID NO:32), with the entirepromoter-hygromycin resistance gene-terminator sequence flanked by 27base pair identification sequences on the 5′ (SEQ ID NO:47 5′ID) and 3′(SEQ ID NO:48 3′ID) ends to yield the DNA fragment referred to as the“Hyg Resistance Cassette” (SEQ ID NO:44, HygR Cassette).

For targeted knockout of the ZnCys-2845 (Naga_100104 g18) locus, Cas9Editor line GE-6791 was transformed by electroporation using 5 μg ofpurified chimeric guide RNA targeting the ZnCys-2845 gene and 1 μg ofthe selectable donor DNA (Hyg Resistance Cassette; SEQ ID NO:44, shownin FIG. 4A) essentially as described in US 2014/0220638. Followingelectroporation, cells were plated on PM124 agar media containinghygromycin to select for transformants that incorporated the hygromycinresistance cassette. Transformants were patched onto a fresh plate andscreened by colony PCR for insertion of the donor fragment into theZnCys-2845 gene.

For colony PCR screening, a small amount of cells from a colony to bescreened was suspended into 100 μl of 5% Chelex 100 Resin (BioRad)/TEsolution and the suspension was boiled for 10 minutes at 99° C., afterwhich the tubes were briefly spun. One microliter of the lysatesupernatant was added to a PCR reaction mix, in which the PCR mixtureand reactions were set up and performed according to the QIAGEN FastCycling PCR Master Mix Protocol from the manufacturer (Handbookavailable at qiagen.com). The primers used to detect the insertion ofthe donor fragment into the targeted locus of the ZnCys-2845 gene wereSEQ ID NO:49 and SEQ ID NO:50. Based on the PCR-based colony screening,two knockout strains, GE-8564 and GE-8565, were tested in productivityassays.

As described below, mutants harboring the HygR cassette in the codingsequence of genome locus Naga_100104 g18 had an insertion of the donorcassette in a gene encoding a predicted Zn(II)2Cys6 binuclear clusterdomain protein (Pfam PF00173, see FIG. 5) and is referred to asZnCys-2845. These mutants exhibited a marked increase in lipidaccumulation with respect to wild type as assessed by FAME/TOC (Example4, FIG. 7C). As described below, the lipid accumulation phenotype inthese ZnCys-2845 KO mutants was further confirmed to be similar to thatobserved in nitrogen-starved wild type cells by the appearance ofprominent lipid droplets (FIGS. 7 F-H).

Example 4 ZNCYS-2845 Knockout Mutants in Batch Productivity Assay

To determine the effect of knocking out the ZnCys-2845 gene on growthand lipid production, ZnCys-2845 knockout strain GE-8564 and the wildtype progenitor strain WT-3730 were cultured in a batch productivityassay in nitrogen replete medium PM123 that included 15 mM nitrate asthe sole nitrogen source available to the cells, i.e., the culturemedium had no source of reduced nitrogen. Because it had been determinedthat the ZnCys-2845 mutant does not grow in the absence of reducednitrogen, the production cultures were inoculated to an initial OD730 of0.5 from seed (scale-up) cultures that were grown in PM124 medium thatincluded 5 mM ammonium in addition to 8.8 mM nitrate.

After inoculation, ZnCys knockout strain GE-8564 and wild type strainWT-3730 were grown in triplicate cultures in a batch assay in 75 cm²rectangular tissue culture flasks containing 175 ml of PM123 medium,which includes 15 mM nitrate as the sole nitrogen source, for sevendays. The flasks were positioned with their narrowest “width” dimensionagainst an LED light. The culture flasks were masked with an opaquewhite plastic to provide a 21.1 cm² rectangular opening for irradianceto reach the cultures. Incident irradiance was programmed at a 16 hlight:8 hour dark cycle with a linear ramp up of irradiance from 0 to1200 uE over 4 hours, after which the irradiance was held at for sixhours at 1200 uE, and then a linear ramp down in irradiance from 1200 to0 uE over a 4 h period (increasing in 15 min intervals) (FIG. 6A).Deionized H₂O was added to the cultures daily to replace evaporativelosses. The temperature of the cultures was regulated by a water bathset at 25° C. Cultures were inoculated at OD730 of 0.5 on day 0 andsamples (5 mls) were removed on days 3, 5, and 7 for assessing celldensity, fatty acid methyl esters (FAME) as a measure of lipid, andtotal organic carbon (TOC). Sampling was done 30 minutes prior to theend of the light cycle. FAME analysis was performed on 2 mL samples thatwere dried using a GeneVac HT-4X. To each of the dried pellets thefollowing were added: 500 μL of 500 mM KOH in methanol, 200 μL oftetrahydrofuran containing 0.05% butylated hydroxyl toluene, 40 μL of a2 mg/ml C11:0 free fatty acid/C13:0 triglyceride/C23:0 fatty acid methylester internal standard mix and 500 μL of glass beads (425-600 μmdiameter). The vials were capped with open top PTFE septa-lined caps andplaced in an SPEX GenoGrinder at 1.65 krpm for 7.5 minutes. The sampleswere then heated at 80° C. for five minutes and allowed to cool. Forderivatization, 500 μL of 10% boron trifluoride in methanol was added tothe samples prior to heating at 80° C. for 30 minutes. The tubes wereallowed to cool prior to adding 2 mL of heptane and 500 μL of 5 M NaCl.The samples were vortexed for five minutes at 2K rpm and finallycentrifuged for three minutes at 1K rpm. The heptane layer was sampledusing a Gerstel MPS Autosampler. Quantitation used the 80 μg of C23:0FAME internal standard. The samples were run on an Agilent 7890A gaschromatography system using an Agilent 127-3212 DB-FFAP, 10 m×100 μm×100nm column and an FID detector at 260° C. The flow rate was 500 μL/minuteusing H₂ as a carrier with constant flow control. The oven was set at90° C. for 0.98 min, then 15.301° C./minute to 230° C. and held for 1.66min. The inlet contained a 4 mm glass wool packed liner (Agilent P/N5183-4647), and was set at 250° C. and used a split ratio of 40:1. Theinjection volume was 900 nL.

Total organic carbon (TOC) was determined by diluting 2 mL of cellculture to a total volume of 20 mL with DI water. Three injections permeasurement were injected into a Shimadzu TOC-Vcsj Analyzer fordetermination of Total Carbon (TC) and Total Inorganic Carbon (TIC). Thecombustion furnace was set to 720° C., and TOC was determined bysubtracting TIC from TC. The 4 point calibration range was from 2 ppm to200 ppm corresponding to 20-2000 ppm for non-diluted cultures with acorrelation coefficient of r²>0.999.

The results of these analyses are shown in Tables 4-6. Values providedfor wild type and knockout GE-8564 mutant are the average of threecultures with standard deviations (sd). The “% increase” column refersto the percentage increase of the ZnCys knockout mutant with respect towild type values.

TABLE 4 Lipid (FAME) Produced by ZnCys-2845 Knockout Mutant and WildType Cultures in Batch Assay with Nitrate-Only Culture Medium WT-3730(NO3) ZnCys-KO GE-8564 (NO₃) Day μg/ml sd μg/ml sd % increase 3 105.039.71 188.56 6.52 79.53 5 140.01 13.48 223.41 0.28 59.57 7 198.49 2.04250.76 3.22 26.33

TABLE 5 Biomass (TOC) Produced by ZnCys-2845 Knockout Mutant and WildType Cultures in Batch Assay with Nitrate-Only Culture Medium WT-3730(NO3) ZnCys-KO GE-8564 (NO3) Day μg/ml s.d. μg/ml s.d. % diff 3 375.610.18 261.7 7.07 −30.3 4 474.6 8.34 283.95 3.61 −40.2 5 534.45 43.20269.5 3.68 −49.6 6 644.8 48.65 311.75 3.18 −51.7 7 804.35 36.13 329.31.70 −59.1

TABLE 6 FAME/TOC Ratios of ZnCys-2845 Knockout Mutant and Wild TypeStrains in Batch Assay with Nitrate-Only Culture Medium WT-3730 (NO3)ZnCys-KO GE-8564 (NO3) Day s.d. s.d. % increase 3 0.28 0.018 0.72 0.044157 5 0.26 0.004 0.83 0.012 219 7 0.25 0.009 0.76 0.006 204

The same batch productivity assay was performed on ZnCys-2845 cas9knockout mutant GE-8564 using PM124 medium that included 5 mM ammoniumin addition to 8.8 mM nitrate. Samples were removed as described andanalyzed for FAME and TOC as provided above. The “% difference” columnrefers to the percentage difference of the ZnCys knockout mutant withrespect to wild type values.

TABLE 7 FAME Produced by ZnCys-2845 Knockout Mutant and Wild TypeCultures in Batch Assay with Nitrate Plus Ammonium Culture MediumZnCys-KO GE-8564 WT-3730 (NO3 + NH4) (NO3 + NH4) DAY μg/ml s.d. μg/mls.d. % diff 3 93.03 6.943 88.43 1.827 −4.9 4 120.14 8.427 124.41 0.4723.6 5 121.31 0.7895 123.31 3.702 1.6 6 169.70 6.0668 181.6 3.397 7.0 7198.11 7.954 225.6 4.548 13.88

TABLE 8 Biomass (TOC) Produced by ZnCys-2845 Knockout Mutant and WildType Cultures in Batch Assay with Nitrate Plus Ammonium Culture MediumWT-3730 ZnCys-KO GE-8564 (NO3 + NH4) (NO3 + NH4) DAY μg/ml s.d. μg/mls.d. % diff 3 321.5 35.07 302.7 6.36 −5.8 4 392.3 16.69 415.65 11.10 6.05 464 4.384 502.3 5.80 8.3 6 556.45 20.15 637.65 14.21 14.59 7 679.956.01 728.6 32.10 7.15

TABLE 9 FAME/TOC Ratios of ZnCys-2845 Knockout Mutant and Wild TypeStrains in Batch Assay with Nitrate Plus Ammonium Culture Medium WT-3730ZnCys-KO GE-8564 (NO3 + NH4) (NO3 + NH4) Day s.d. s.d. % diff 3 0.290.0100 0.29 0.0001 0 4 0.31 0.0085 0.30 0.0091 −3.2 5 0.26 0.0008 0.250.0045 −3.8 6 0.31 0.0220 0.29 0.0117 −6.5 7 0.29 0.0091 0.31 0.0074 6.9

The graphs in FIGS. 7A-7D show the results of this analysis. FIG. 7Ademonstrates that cultures of ZnCys-2845 knockout strain GE-8564(average values for triplicate cultures depicted as circles on thegraph) grown in a medium that included only nitrate as a nitrogen sourcehad higher FAME content than wild type cultures every day tested. As canbe seen in Table 4, these FAME values were considerably higher than wildtype on a volumetric basis. Although the FAME content of the ZnCys-2845knockout mutant culture in nitrate-only medium was at a higher level onday 3 of the culture, which was the first day assayed, as well as ondays 5 and 7 (Table 4 and FIG. 7A), the increase in FAME per day betweendays 3 and 7 was less for the ZnCys-2845 knockout strain than for thewild type strain. FIG. 7B demonstrates that over this time period theZnCys-2845 gene disruption mutant cultured in nitrate-only medium(circles) increased its total organic carbon very little as compared towild type (Xs), which showed steady growth as assessed by TOCaccumulation (as also seen in Table 5). Thus, the ZnCys-2845 knockoutstrain, when cultured in a medium that included nitrate as the solenitrogen source, behaved as though it were in nitrogen starvation,increasing lipid production but also decreasing in biomass accumulation.FIG. 7C confirms this, demonstrating that over the course of the oneweek productivity assay, the FAME/TOC ratio of the ZnCys-2845 knockoutstrain GE-8564 was elevated over wild type (approximately three-foldthat of wild type, Table 6), with greater than 60% (and up to at leastabout 80%) of TOC being allocated to FAME lipids. FIG. 7D shows that theC16 and C18 fatty acids that were overproduced in knockout strainGE-8564 (black bars) with respect to wild type in nitrogen repleteconditions (diagonally striped bars), while C20 fatty acids wereunderrepresented with respect to their abundance in wild type cells, asexpected for selective overproduction of storage lipids (i.e.,triglycerides). The fatty acid profile of the GE-8564 knockout strainwas very similar to that of wild type cells under nitrogen starvation(dotted bars).

Direct demonstration of TAG production was determined by analysis ofextracted lipids. Extracted lipids of knockout mutant GE-8564 and wildtype progenitor strain WT-3730 from samples taken on Day 7 of the batchassay in the nitrate-only PM074 medium were identified and quantitatedby HPLC. For HPLC analysis of lipids, 2 mL samples of each culture werespun down at maximum speed for 5 minutes, the supernatants were removed,and pellets were re-suspended in 400 μL of H₂O. The cell suspensions(approximately 500 μL) were transferred to 4 mL glass vials with Teflonlined caps. 500 μL of glass beads (212-300 μm diameter) were added toeach of the cell suspensions, after which 50 μL of 50% H₂SO₄ and 100 μLof 5M NaCl were added. Bead beating was performed for 5 minutes at 1krpm, then 2 mL of hexane was added to each sample, and bead beating wasrepeated for 5 minutes at 1 krpm. The samples were loaded onto amulti-tube vortexer and shaken for 30 minutes at 1 krpm, and thenvortexed for 30 seconds at 2.5 krpm. 500 μL of the organic layer wastransferred to an HPLC vial, and 50 μL of internal standard solution (1mg/mL 6-ketocholestanol in toluene) was added to each vial. Standardswere from NuCheck, Sigma-Aldrich, or Supelco. The vials were capped andvortexed briefly (5 seconds at 2.5 krpm) prior to HPLC analysis. TheHPLC was run at a flow rate of 2 mL/minute on a Chromegasphere SI-60 150mm×4.6 mm×10 μm column (ES Industries), with a column compartment set at40° C. The injection volume was 25 μL with a draw and eject speed of 200μL/minute. Eluent A was hexane and Eluent B was a 80:10:10:1 mixture ofhexane, isopropanol, ethyl acetate, and 10% formic acid in isopropanol,run as a gradient program as follows: 2% B at 0.0 min; 2% B at 1.0 min;25% B at 5.0 min; 98% B at 5.5 min; 98% B at 8.99 min; 2% B at 9.00 min;stop time: 9.0 minutes; 4 minutes post time. The detector was ELSD at30° C. and 3.5 bar N2, with a gain of 5.

FIG. 7E shows that the amount of TAG in the ZnCys-2845 knockout cells innitrate only medium was more than 5-fold that of the wild type cells,that is, the observed increase in FAME lipid could be attributed to theincrease in TAGs. Electron microscopy also showed the dramatic lipidaccumulation characteristic of the nitrogen starvation response. FIG. 7Fshows a wild type cell grown under nitrogen replete conditions(nitrate-only culture medium), with a prominent nucleus (N), chloroplast(Ch), and mitochondrion (M), as well as a few small lipid droplets (LD).FIG. 7G shows the ZnCys knockout mutant grown in nitrate-only medium, inwhich a prominent lipid droplet (LD) is the largest cellular structurevisible, a cellular morphology highly similar to the nitrogen starvedwild type cell shown in FIG. 7H. Thus, the ZnCys-2845 polypeptide actsas a negative regulator of lipid biosynthesis, as attenuating expressionof the ZnCys-2845 gene results in increased lipid production.

The increase in FAME exhibited by the ZnCys-2845 knockout straincultured in nitrate-only medium was not apparent when the ZnCys-2845knockout strain was grown in a culture medium that also includedammonium however (Table 7). In this case, the amount of FAME producedwas very similar to that produced by wild type cells grown in nitrateplus ammonium medium, with lipid production of the knockout mutantincreasing somewhat relative to wild type toward the end in the run,probably indicating depletion of ammonium from the batch culture (Table7). FIG. 8A shows that the amount of FAME produced by wild type(diamonds) and the ZnCys-2845 knockout strain (circles) cultured inammonium-only medium was virtually identical over the one week batchassay, as was TOC accumulation, shown in FIG. 8B (also evident fromTable 8). FAME/TOC values of the wild-type and ZnCys-2845 knockoutstrain were correspondingly similar (FIG. 8C, Table 9).

Thus, the ZnCys-2845 gene disruption mutant behaved like the wild typestrain when ammonium was replete in the culture medium (Tables 7-9 andFIGS. 8A-8C), but appeared to be impaired in nitrate assimilation,behaving as though the cells were in nitrogen depleted medium whennitrate was the sole source of nitrogen present by inducing storagelipid biosynthesis (FIGS. 7A-7H).

Example 5 Bioinformatic Analysis of the ZNCYS-2845 Protein: Domains andOrthologs

As described in Example 1, the ZnCys-2845 gene at locus Naga 100104 g18that was differentially expressed between the N-replete and N-depletesamples was a gene (cDNA sequence provided as SEQ ID NO:1) encoding apolypeptide (SEQ ID NO:2) that appeared on a bioinformatics-generatedNannochloropsis putative transcription factor list. The polypeptide wasobserved to have a Zinc(2)Cys(6) domain characteristic of sometranscription factors and is therefore classified as a Zn(2)-C(6)fungal-type DNA-binding domain protein. In addition to the Zn(2)-Cys(6)domain, the Nannochloropsis polypeptide ZnCys-2845 contains a distinctnuclear localization sequence with a confidence score of 1.0 (whichequates to 100% confidence), consistent with its characterization astranscription factor (FIG. 5).

ZnCys-2845 is a 1065 amino acid protein (SEQ ID NO:2) identified bytranscriptomics analysis of genes differentially regulated during lipidinduction and annotated as a putative transcription factor due to theZn(2)-Cys(6) binuclear cluster domain extending from amino acid 190 to219 (SEQ ID NO:3). The protein recruits to Pfam PF00172 (“Zn_Clus” or“Fungal Zn(2)-Cys(6) binuclear cluster domain” with a bit score of 25.2(the gathering cutoff for this family is 20.8) and an e value of 1.1e-05. Thus, ZnCys-2845 is a member of the Zn(II)2Cys6 fungal-typeDNA-binding domain protein family. Members of this family contain thewell-conserved motif CysX₂CysX₆CysX_(5_12)CysX₂CysX_(6_8) Cys (acysteine residue followed by two amino acid residues of any identity,followed by second cysteine residue followed by six amino acid residuesof any identity, followed by a third cysteine residue followed bybetween five and twelve amino acid residues of any identity, followed bya fourth cysteine residue followed by two amino acid residues of anyidentity, followed by a fifth cysteine residue followed by between sixand eight amino acid residues of any identity, followed by a sixthcysteine residue; SEQ ID NO:4). It has been demonstrated that thecysteine residues can bind two zinc atoms, which coordinate folding ofthe domain involved in DNA binding. Other identifiers for this domaininclude the conserved domain database (cdd) domain cd00067, the interproprotein domain database domain IPR001138, the SMART protein domain‘GAL4’, and the PROSITE protein domain PS00463.

This class of “ZnCys” transcription factors was originally thought to beexclusively fungal, but more recently members have been identified amongchromalveolates, in particular stramenopiles/heterokonts (includingnon-photosynthetic labyrinthulomycetes or “chytrids”) and haptophytes(e.g., E. huxleyi). The first and best studied protein in this family isGal4p, a Saccharomyces transcriptional activator of genes involved ingalactose catabolism (Leverentz & Reece (2006) Biochem Soc Transac34:794-797; Breunig (2000) Food Technol. Biotechnol. 38:287-293). Theterms “Zn(2)-C(6) fungal-type DNA-binding domain protein”, “Zn(II)2Cys6fungal-type DNA-binding domain protein”, “Zn(2)-Cys(6) domainpolypeptide”, “Zn(2)Cys(6) protein/polypeptide” and “Zn2Cys6protein/polypeptide” are used interchangeably herein.

Examination of genome databases revealed genes encoding polypeptideshaving Zn(2)-Cys(6) domains in plants and fungi. Interestingly, severalheterokont species were found to include Zn(2)-Cys(6) domainpolypeptides, including labyrinthulomycete species such as from thegenera Schizochytrium and Aplanochytrium and diatom species, includingmembers of the Navicula, Cyclotella, Thalassiosira, Phaeodactylum,Fragilariopsis genera.

TABLE 10 Putative Orthologs of N. gaditana Lipid Regulator ZnCys-2845SEQ Translation ID Species Library ID NO Phaeodactylum triconutumPhatr2_2 337562 5 Navicula sp. wt0229_cDNA_clc 4242909 6 Navicula sp.wt0229_cDNA_clc 4243087 7 Navicula sp. wt0229_cDNA_clc 4238609 8Cyclotella sp. wt0293_nuclear_v1.3 5077789 9 Cyclotella sp.wt0293_nuclear_v1.3 5083384 10 Cyclotella sp. wt0293_nuclear_v1.35084316 11 Thalassiosira pseudonana thaps3_2 322124 12 Thalassiosirapseudonana thaps3_2 326683 13 Thalassiosira pseudonana thaps3_2 32693714 Fragilariopsis cylindrus fracy1_2 386612 15 Fragilariopsis cylindrusfracy1_2 386837 16 Nannochloropsis oceanica Wt-5473 17

The N. oceanica gene (coding sequence provided as SEQ ID NO:84, encodedpolypeptide provided as SEQ ID NO:17) was found by scanning thepredicted protein set of a proprietary Nannochloropsis genome formatches to the PF00172 HMM model using hmmsearch (hmmer.org) and thetrusted cutoff for the match score; however, no additionalNannochloropsis orthologs were found by scanning Nannochloropsis genomesdownloaded fromsinglecellcenter.org/en/NannoRegulationDatabase/Download/S11.zip,probably due to incomplete protein sets of the genomes. Additionalputative orthologs of the Nannochloropsis gaditana ZnCys-2845 protein(SEQ ID NO:2) were found by BLAST (tblastn) against public genomeassemblies of Nannochloropsis strains and species, including N. gaditanastrain CCMP526, N. oceanica strain IMET1, N. oceanica strain CCMP531, N.oculata strain CCMP525, N. salina strain CCMP537, and N. granulatastrain CCMP529. However, in each case the alignment matches wereobserved to break within the PF00172 Zn_Clus domain, such that all ofthe sequences were found to be incomplete, lacking the 5′ end of thecoding region and N-terminal sequence of the proteins. An additionalconserved region, approximately 170 amino acids in length from theZnCys-2845 polypeptide (positions 345-51 of SEQ ID NO:27), was clearlyidentified in all Nannochloropsis genomes analyzed and examined further.The delta-blast tool in NCBI was used to evaluate the highly conservedregion between N. gaditana WT-3730 ZnCys-2845 (SEQ ID NO:2) putativeorthologs in other Nannochloropsis species.

This domain, a PAS3_fold domain (pfam PF08447), is found in manysignaling proteins where it functions as a signal sensor. Using thisapproach putative matches to ZnCys-28345 could be clearly identified ineach of the six Nannochloropsis genomes searched. Unfortunately, thealignment matches in all cases appeared to break within the putativematch to the PF00172 Zn_Clus domain. However, from the blast alignments,an approximately 170 aa region from ZnCys-28345 (positions 345-517) wasobserved and clearly identifiable across all strains (single copy). Analignment of the PAS3 domains in the identified ZnCys-2845 orthologsfrom Nannochloropsis is provided in FIG. 9, where the high degree ofconservation of the domain sequence among different Nannochloropsisspecies is evident. The PAS3 domain of ZnCys-2845 (identified in thegene diagram of FIG. 12A) extends from amino acid 345 to amino acid 517of SEQ ID NO:2, and is provided as SEQ ID NO:21. SEQ ID NO:21 alsorepresents the sequence of the PAS3 domain of N. gaditana strainCCMP526. The sequence of the PAS3 domain of N. oceanica strain WT-5473,N. oceanica strain IMET1, and N. oceanica strain CCMP531 ZnCys-2845orthologs is provided as SEQ ID NO:22. The N. oceanica ZnCys-2845ortholog PAS3 domain (SEQ ID NO:22) is 86% identical in sequence to theN. gaditana PAS3 domain (SEQ ID NO:21). The PAS3 domain of the N. salinastrain CCMP537 ZnCys-2845 ortholog is provided as SEQ ID NO:23, which is98% identical to the N. gaditana ZnCys-2845 PAS3 domain (SEQ ID NO:21).The PAS3 domain of the N. oculata strain CCMP539 ZnCys-2845 ortholog isprovided as SEQ ID NO:24, and it demonstrates 86% sequence identity tothe PAS3 domain of N. gaditana ZnCys-2845 (SEQ ID NO:21). As providedabove, the PAS3 domain of the ZnCys-2845 ortholog of N. granulata strainCCMP529 is provided as SEQ ID NO:22, which is approximately 86%identical to the PAS3 domain of N. gaditana ZnCys-2845 (SEQ ID NO:21).

An alignment of the amino acid sequence encoded by the N. gaditanaZnCys-2845 gene and the amino acid sequence (SEQ ID NO:17) encoded bythe N. oceanica strain WT-5473 ortholog of the ZnCys-2845 gene, both ofwhich were determined by in-house genome sequencing and gene assignment,is provided in FIG. 10. Genome sequences of three additionalNannochloropsis species, N. granulata strain CCMP529, N. oculata strainCCMP539, and N. salina strain CCMP537, were further examined to attemptto stitch together protein-encoding sequences of putative ZnCys-28545orthologs as characterized by the PAS3 domains. The six Nannochloropsisgenomes were curated to find regions of homology extending outward fromthe PAS3 domains. Blastn was utilized to identify homologous sequences,which were linked together with gaps introduced to maximize homology.

The Zn(2)-Cys(6) domain of N. oceanica is identical to the Zn(2)-Cys(6)domain of N. gaditana (SEQ ID NO:3). The polypeptides encoded by the twogenes (N. gaditana ZnCys-2845 and the N. oceanica ortholog) have 56%identity across the entire deduced polypeptide sequence, and 71%identity across the first 517 amino acids of N. gaditana ZnCys-2845 (SEQID NO:2), a portion of the amino acid sequence that extends from theN-terminus of the protein through the Zn(2)-Cys(6) domain and throughthe PAS3 domain (see FIG. 5). Amino acids 1-200 encoded by the N. salinaZnCys-2845 homologous sequence (SEQ ID NO:20) have approximately 98%identity to corresponding amino acid sequence of N. gaditana ZnCys-2845(SEQ ID NO:2); whereas the incomplete polypeptide sequence of a putativeortholog of N. granulata (SEQ ID NO:18) is approximately 61% identicalto N. gaditana ZnCys-2845 (SEQ ID NO:2) and the incomplete polypeptidesequence of a putative ortholog of N. oculata (SEQ ID NO:19) isapproximately 61% identical to N. gaditana ZnCys-2845 (SEQ ID NO:2).These partial polypeptide sequences do not include the PAS3 domains ofthe Nannochloropsis orthologs, which, as noted above, have much higher %identities to the PAS3 domain of N. gaditana ZnCys-2845 (SEQ ID NO:21).

Example 6 Growth and Lipid Biosynthesis of ZNCYS-2845 Knockout Mutant inSemi-Continuous Production System Using Urea Nitrogen Source

To determine whether the ZnCys-2845 gene disruption knockout mutantcould utilize other sources of nitrogen, a semi-continuous productivityassay was set up in which the culture medium included urea as the solenitrogen source.

For assays in cultures that included urea as the sole nitrogen source,seed cultures (also referred to as “starter cultures” or “scale-upcultures”) of ZnCys-2845 knockout strain GE-8564 and wild type strainWT-3730 were grown in PM125 medium that included 7.5 mM urea as the solenitrogen source. For assays in which wild type cells were cultured innitrate-only medium (PM074), the wild type cells were scaled up incultures that included the PM074 nitrate-only medium. The GE-8564ZnCys-2845 knockout mutants were scaled up in cultures that included thePM124 medium that included both nitrate (8.8 mM) and ammonium (5 mM) forthe semi-continuous assays that included only nitrate as the nitrogensource in the assay culture medium.

The scale-up cultures were used to inoculate 225 cm² rectangular tissueculture flasks, each of which contained a final total volume of 550 mlof culture after inoculation. The cultures were inoculated so that each550 ml culture had an initial OD₇₃₀ of 0.9. A typical inoculum volumewas approximately 200 ml of scale-up culture that was added toapproximately 350 ml of assay culture medium, which was either PM074(nitrate-only medium) or PM125 (urea-only medium) Cultures were diluteddaily at mid-day, when the light intensity was at its peak, by removing30% of the volume (165 mls) and replacing it with the same volume of theassay medium (either PM074 or PM125) plus an additional 10 ml ofdeionized water to make up for evaporation (included in the make-upmedium). Semi-continuous assays were typically run for 10-14 days. Dailylipid and biomass productivities were only calculated for cultures thathad reached steady state (where the increase in growth was equal to thedilution factor for the assay).

Three cultures were initiated per strain. The flasks included stir barsand had stoppers having inserted tubing connected with syringe filtersfor delivering CO₂ enriched air (1% CO₂, flow rate, 300 ml per min) thatwas bubbled through the cultures. The flasks were set in a water bathprogrammed to maintain a constant temperature of 25° C. on stir platesset to 575 rpm during the assay period. Culture flasks were masked withan opaque white plastic to provide a 31.5 cm² rectangular opening forirradiance to reach the culture. The flasks were aligned with the width(narrowest dimension) against an LED light bank that was programmed witha light/dark cycle and light profile that increased until “solar noon”and then declined to the end of the light period. The light profile wasdesigned to mimic a spring day in Southern California: 14 h light:10 hdark, with the light peaking at approximately 2000 μE (FIG. 6B). Theflasks included stir bars and had stoppers with inserted tubingconnected with syringe filters for delivering CO₂ enriched air (1% CO₂,flow rate, 300 ml per min). The flasks were set in a water bathprogrammed to maintain a constant temperature of 25° C. on stir platesset to 575 rpm during the assay period.

Cultures were diluted daily at mid-day, when the light intensity was atits peak by removing 30% of the volume (165 ml) and replacing it withthe same volume of the assay medium plus an additional 10 ml ofdeionized water to make up for evaporation. A 30% dilution rate wasempirically determined as the most productive dilution rate forNannochloropsis, as 50, 30, and 15% daily dilutions resulted in averageTOC productivities of 6.5, 9 and 8 g/m²/day, respectively.Semi-continuous assays were typically run for 7-14 days. Daily lipid(FAME) and biomass (TOC) productivities were calculated from culturesthat had reached steady state standing crop TOC and FAME density.Volumetric FAME and TOC productivities in (mg/L/day) were calculated bymultiplying the volumetric FAME and TOC amounts by the 30% dilutionrate. Aerial productivities (g/m2/day) were calculated by dividing thetotal productivity of the culture by the size of the aperture throughwhich irradiance was permitted:

${\frac{( {{volumetric}\mspace{14mu} {productivity}} )\mspace{14mu} {mg}}{L*{day}}*\frac{0.55\mspace{14mu} L}{0.00315\mspace{14mu} m^{2}}*\frac{g}{1000\mspace{14mu} {mg}}} = \frac{g}{m^{2}*{day}}$

FIG. 11A shows that the ZnCys-2845 knockout mutant GE-8564, whencultured in the semi-continuous assay where nitrate is the sole sourceof nitrogen (diamonds), showed a large induction of lipid production atthe outset of the assay which subsequently declined steeply after day 3of the assay such that lipid production fell below that of thenon-induced wild type culture by day 10 of the assay, after which itdeclined to even lower levels. This pattern is consistent with theresults of the batch assay of Example 4 which indicated the ZnCys-2845knockout mutant GE-8564 is induced for lipid production in nitrate-onlymedia.

In contrast, the cultures of the GE-8564 mutant having a disruptedZnCys-2845 gene cultured in urea-only medium (FIG. 11A, circles) hadconsistently higher daily FAME productivity than the wild type straincultured in either nitrate only medium (triangles) or urea-only medium(squares), both of which are conditions in which the wild type strain isnot induced for lipid production (as evidenced by the FAME/TOC ratios ofthese cultures throughout the assay, see FIG. 11C and Table 14, below).Table 11 provides the daily amounts of FAME produced on an areal basisby all strains in the semi-continuous assay along with the percentageincrease of the amount of FAME produced by the knockout mutant GE-8564strain over wild type FAME levels when both were cultured in urea-onlyculture medium also provided. Average areal FAME productivity for eachstrain, expressed as g/m²/day, is provided in Table 12. The increase inFAME productivity of the knockout mutant strain GE-8564 over the wildtype strain averaged 58% over the course of the thirteen-day assay whenboth strains were cultured in urea-only medium. It can also be seen thatwild type cells cultured in urea-only medium showed, on average, 16%less FAME productivity than wild type cells in nitrate-only medium. TheGE-8564 knockout mutant in nitrate-only medium showed increased FAMEproduction with respect to wild type in the first 8 days of the assayand then experienced declines in daily FAME production as the assayprogressed, consistent with a nitrogen depletion response.

TABLE 11 FAME (g/m²/day) Produced by ZnCys Knockout and Wild typeStrains Cultured with Nitrate or Urea as Nitrogen Source in Semi-Continuous Assay ZnCys-KO ZnCys- % ZnCys- ZnCys-KO WT/ KO/ differenceWT/ KO/ % increase DAY NO3 NO3 NO3 UREA UREA UREA 1 2.48 5.46 120% 1.842.64 43% 2 2.41 5.86 143% 2.24 2.70 20% 3 2.45 6.68 172% 2.18 3.08 41% 42.23 6.40 187% 2.00 2.80 40% 5 2.45 5.41 121% 1.98 3.05 54% 6 2.40 4.72 97% 2.12 3.57 69% 7 2.46 3.85  57% 1.90 3.55 87% 8 2.47 3.18  28% 2.113.46 64% 9 2.54 2.43  −5% 2.07 3.39 64% 10 2.38 1.77 −26% 1.90 3.16 66%11 2.25 1.27 −43% 1.74 3.25 87% 12 2.35 0.90 −62% 1.89 3.09 63% 13 2.090.69 −67% 1.90 3.05 60% Avg. 2.38 3.74  57% 1.99 3.14 57%

Table 12 provides the average daily FAME productivities of the culturesover the thirteen day semi-continuous culture. The average daily FAMEproductivity for the ZnCys knockout GE-8564 grown in a urea-only mediumwas 32% higher than the average daily FAME productivity of the wild typestrain (WT-3730) grown in nitrate medium (rightmost column). The highFAME productivity value of the ZnCys-2435 knockout in nitrate-onlymedium is due to the very high FAME production in the first 7 days ofthe culture. The daily FAME productivity is already declining by day 5of the culture however, after which it declines well below wild typecultured in nitrate-only medium (FIG. 11A).

TABLE 12 Average Daily FAME Productivity of Semi-Continuous Cultures inUrea-Only or Nitrate-Only Media g/m²/day Avg change Strain FAME v. WT(NO₃) WT-3730 (NO3) 2.38  0% WT-3730 (Urea) 1.99 −16% ZnCys-KO GE-85643.14   32% (Urea) ZnCys-KO GE-8564 3.74   57% (NO3)

FIG. 11B shows that the ZnCys-2845 knockout mutant (GE-8564) cultured inthe semi-continuous assay in a nitrate-only medium (diamonds)demonstrated a precipitous drop in biomass production over the course ofthe assay, declining to levels that were only a fraction of the biomassproduced by wild type cells cultured in nitrate medium by the end of theassay. In contrast, during this semi-continuous productivity assay,there was little decline in biomass (TOC) productivity in the ZnCys-2845gene disruption mutant cultured in urea medium (circles) with respect tothe wild type strain cultured in nitrate medium (triangles), and theZnCys-2845 knockout mutant even demonstrated slightly betterproductivity than wild type cultured in urea medium (squares), all threeof which remained in fairly consistent over the entire course of theassay.

Table 13 provides the TOC content of these semi-continuous cultures andthe percentage difference in the daily amount of TOC produced betweenthe ZnCys-2845 knockout mutant cultured in nitrate-only medium withrespect to wild type cells cultured in nitrate-only medium, and thepercentage difference in daily TOC produced between the ZnCys-2845knockout mutant cultured in urea medium with respect to wild type cellscultured in urea medium. In Table 13 the reduction in the amount ofbiomass produced on a daily basis can be seen in ZnCys-2845 knockoutmutant cultured in nitrate only medium as the assay progresses. Thebiomass production levels of the other cultures, including theZnCys-2845 knockout mutant cultured in urea medium that had a 58%increase in daily FAME productivity with respect to wild type in ureamedium, remains quite consistent throughout the thirteen day assay, andhas a slightly better average TOC productivity than does the wild typestrain cultured in urea medium. Thus, the ZnCys-2845 knockout mutant wasable to accumulate biomass at levels at least equivalent to the wildtype strain while demonstrating nearly 60% higher daily FAMEproductivity when cultured in a medium that included urea as the solesource of nitrogen.

TABLE 13 Biomass (g/m²/day TOC) Produced by Strains Grown in Nitrate orUrea in a Semi-Continuous Assay ZnCys- ZnCys- KO % KO % WT/ ZnCys-difference WT/ ZnCys- increase, NO3 KO/NO3 NO3 UREA KO/UREA UREA DAYmedium medium medium medium medium medium 1 9.65 11.00  14% 8.06 8.8610% 2 9.24 9.69   5% 7.94 8.25  4% 3 9.42 9.61   2% 8.35 8.80  5% 410.28 8.72 −15% 9.21 8.86 −4% 5 10.08 7.19 −29% 8.85 8.88  0% 6 9.976.18 −38% 8.72 9.09  4% 7 9.99 5.07 −49% 8.79 9.29  6% 8 9.42 3.83 −59%8.03 8.55  6% 9 9.34 3.22 −66% 7.99 8.84 11% 10 9.12 2.46 −73% 7.94 8.57 8% 11 9.32 2.00 −79% 7.74 8.74 13% 12 9.53 1.77 −81% 8.11 8.59  6% 139.57 1.45 −85% 8.28 9.25 12% Avg 9.61 5.55 −42% 8.31 8.81  6%

In fact, despite the increased lipid production by the ZnCys-2845knockout mutant in urea-only medium with respect to wild type cells innutrient replete (nitrate-only) medium (FIG. 11A and Table 11) theaverage amount of TOC produced throughout the course of the assay by theZnCys knockout mutant in urea-containing medium was at least 90% that ofwild type cells cultured in nitrate medium, i.e., only about 10% lessthan that of nitrogen replete wild type cells.

FIG. 11C shows the daily FAME to TOC ratios of the cultures in thesemi-continuous assay. These ratios stay fairly consistent for allsamples with the exception of the ZnCys-2845 gene disruption mutant(“ZnCys-KO”) cultured in nitrate-only medium (diamonds), which showsFAME to TOC ratios climbing from the first day of culturing up to day 8,after which the ratio begins to decline. These FAME:TOC ratios of theZnCys-2845 gene disruption mutant cultured in nitrate-only medium arefar higher than the FAME: TOC ratios of wild type cultured in bothnitrate-only and urea-only medium and the ZnCys-2845 knockout mutantcultured in urea-only medium and are indicative of the classic lipidinduction response to nitrogen depletion. FAME to TOC ratios of themutant and wild type semicontinuous assay cultures are provided in Table14.

TABLE 14 FAME/TOC Ratios of Cultures Cultured in Nitrate or Urea WT/ZnCys-KO/ WT/ ZnCys-KO/ DAY NO3 NO3 UREA UREA  1 0.3 0.5 0.2 0.3  2 0.30.6 0.3 0.3  3 0.3 0.7 0.3 0.3  4 0.2 0.7 0.2 0.3  5 0.2 0.8 0.2 0.3  60.2 0.8 0.2 0.4  7 0.2 0.8 0.2 0.4  8 0.3 0.8 0.3 0.4  9 0.3 0.8 0.3 0.410 0.3 0.7 0.3 0.4 11 0.2 0.6 0.2 0.4 12 0.2 0.5 0.2 0.4 13 0.2 0.5 0.20.3

The ZnCys-2845 gene disruption mutant cultured in urea-only showsconsistently higher FAME:TOC ratios with respect to wild type cellscultured in either nitrate-only or urea only medium, but the FAME:TOCratio is fairly stable throughout the culture period, in the range of0.3 to less than 0.5, representing an increase of on average about 45%over wild type. Thus, when urea was used as the sole source of reducednitrogen in the assay, the ZnCys-2845 gene disruption mutantdemonstrated significantly increased partitioning of carbon to lipid(Table 14, FIG. 11C) without a substantial loss of overall carbonassimilation (Table 13, FIG. 11B), resulting in an approximately 57%increase in FAME produced on a daily basis and only an approximately 6%decrease in TOC produced with respect to wild type cells cultured underthe same (urea-only) conditions over the course of the assay.

Example 7 CAS9 ZNCYS-2845 Knockdown Constructs

Since the ZnCys-2845 knockout line exhibited a significant deficit inTOC productivity concomitant with increased carbon partitioning to lipidin batch growth (Example 4, FIG. 7B), we next investigated whethervarying the degree of attenuation of ZnCys-2845 expression would resultin engineered strains in which lipid and TOC productivity were betteroptimized. Additional mutant strains were engineered to have decreasedexpression of the ZnCys-2845 gene using Cas9/CRISPR genome engineering.Twelve chimeric guide RNAs were designed to target sequences upstream ofthe ATG, within an intron of the gene, in the 3′ end of the gene butstill within the coding sequence, or in the 3′ untranslated region ofthe gene (FIG. 12A). These constructs described here as “Bash Knockdownconstructs” or simply “Bash constructs” because they are designed toinsert the donor fragment into a site in a region of the gene where theinsertion is expected to allow the targeted gene to be expressed at alower level than in wild type. (Correspondingly, the strains thatinclude such insertions are referred to as “Bash strains”, “Bashers”, or“Bash Knockdown mutants”.) The twelve 18-nucleotide sequences havinghomology to the ZnCys-2845 gene (target site sequences) are provided inTable 15.

TABLE 15 Target and Chimeric Guide Sequences for Attenuating ZnCys-2845Expression “Bash” Gene Attenuation Target Gene Region Target SequenceSite Targeted (18 nt) −1 5′ UTR SEQ ID NO: 51 1 5′ UTR SEQ ID NO: 52 25′ UTR SEQ ID NO: 53 3 5′ UTR SEQ ID NO: 54 4 5′ UTR SEQ ID NO: 55 6Intron in SEQ ID NO: 56 PAS3 domain sequence 7 Intron in SEQ ID NO: 57PAS3 domain sequence 8 C-terminus SEQ ID NO: 58 9 C-terminus SEQ ID NO:59 10 C-terminus SEQ ID NO: 60 11 3′ UTR SEQ ID NO: 61 12 3′ UTR SEQ IDNO: 62

Chimeric guide DNA constructs were synthesized as two complementarystrands that were annealed to produce a double-stranded construct with aT7 promoter positioned upstream of the guide sequence (that included the18-nucleotide target sequence in addition to the tracr sequence), andused to produce the chimeric guide RNAs by in vitro transcription andpurified as described in Example 3. SEQ ID NO:42 is an example of ageneric “sense” strand for producing a guide RNA and SEQ ID NO:43 is anexample of a generic “complementary” strand that would be annealed tothe sense strand (where the target sequence is again represented by 18Ns,) for producing the guide RNA by in vitro transcription.

In the present experiments, each chimeric guide RNA was individuallytransformed into Nannochloropsis Editor strain GE-6791 along with thedonor fragment that included a Hyg resistance (“HygR”) cassette (FIG.4A, SEQ ID NO:44) as described in Example 3. Hygromycin resistantcolonies were selected and screened by colony PCR as described usingprimers adjacent to the targeted regions of the ZnCys-2845 gene. PrimersMA-ZnCys-FP (SEQ ID NO:49) and MA-ZnCys-RP (SEQ ID NO:50) were used toconfirm the knockout (GE-8564) and donor fragment insertion intointrons; primers MA-5′Bash-ZnCys-FP (SEQ ID NO:63) andMA-5′Bash-ZnCys-RP (SEQ ID NO:64) were used to confirm the insertion ofthe donor fragment into the 5′ regions of the ZnCys-2845 gene; andprimers MA-3′Bash-ZnCys-FP (SEQ ID NO:65) and MA-3′Bash-ZnCys-RP (SEQ IDNO:66) were used to confirm the insertion of the donor fragment into the3′ regions of the ZNCys-2845 gene. Eleven of the twelve guide RNAsresulted in isolates that by colony PCR appeared to have the Hyg geneinserted at the targeted locus (insertion into 5′ UTR target site −1 wasnot observed.)

Quantitative reverse transcription-PCR (qRT-PCR) was performed on RNAisolated from the knockdown lines to determine whether expression of theZnCys-2845 gene was in fact reduced in these lines. The ZnCys-2845 BashKnockdown strains were grown under standard nitrogen replete conditions(PM074 (nitrate-only) medium) and harvested during early stationaryphase. Total RNA was isolated from ZnCys-2845 Bash Knockdown cells,using methods provided in Example 1, above. RNA was converted to cDNABioRad's iScript™ Reverse Transcription Supermix kit according to themanufacturer's protocol. For PCR, Ssofast EvaGreen Supermix (Bio-Rad,Hercules, Calif.) was used along with gene-specific primers. The PCRreaction was carried out on C1000 Thermal Cycler coupled with a CFXReal-time System (BioRad). Primer and cDNA concentrations were accordingto the manufacturer's recommendation. Primers for amplifying a sequenceof the ZnCys-2845 transcript were SEQ ID NO:67 and SEQ ID NO:68.Transcript levels for each sample were normalized against a housekeepinggene with consistent expression levels under different cultureconditions (1T5001704; SEQ ID NO:69) and relative expression levels werecalculated using the ddCT method using BioRad's CFX Manager software.

FIG. 12B shows that several of the strains had reduced levels ofZnCys-2845 transcript. Of these, strains GE-13108 (ZnCys-2845 Bash-2)and GE-13109 (ZnCys-2845 Bash-3), targeting the 5′ end of the ZnCys-2845gene, and strain GE-13112 (ZnCys-2845 Bash-12), targeting the 3′ end ofthe ZnCys-2845 gene, were selected for productivity assays.

Example 8 RNAi Knockdown Construct

In another strategy to determine whether decreasing expression of theZnCys-2845 gene would allow the cells to accumulate more carbon than theCas9 knockout while still producing increased amounts of lipid withrespect to wild type, an interfering RNA (RNAi) construct was designedfor expression in Nannochloropsis cells. The construct included asequence designed to form a hairpin that included a sequence homologousto a region of the ZnCys-2845 gene (SEQ ID NO:70), followed by a loopsequence and then followed by the inverse sequence to the ZnCys-2845gene-homologous sequence, driven by the N. gaditana EIF3 promoter (SEQID NO:46) and followed by N. gaditana “terminator 9” (SEQ ID NO:71). Theconstruct also included a gene encoding GFP codon optimized forNannochloropsis (SEQ ID NO:36) under the control of the Nannochloropsis4AIII promoter (SEQ ID NO:37) and followed by “terminator 5” (SEQ IDNO:38), as well as a gene conferring hygromycin resistance (SEQ IDNO:45) driven by the TCTP promoter (SEQ ID NO:34) and terminated by theEIF3 terminator (SEQ ID NO:35). The construct was linearized andtransformed into wild type Nannochloropsis gaditana WT-3730 byelectroporation as described.

Hygromycin resistant colonies were screened for the presence of the RNAiconstruct and positive strains were further screened by qRT-PCR asdescribed in Example 7 for knockdown of the ZnCys-2845 transcriptlevels.

Example 9 Knockdown Constructs in Batch Assay

ZnCys-2845 RNAi strain GE-13103 and ZnCys-2845 knockdown “basher”strains GE-13108, GE-13109, and GE-13112 were tested in the batchproductivity assay described in Example 4 by scaling up the cultures inculture medium PM124 (which includes both NH₄ and NO₃ as nitrogensources) and by carrying out the assay in PM123 culture medium thatincludes nitrate as the sole nitrogen source. The ZnCys-2845 Knockoutstrain GE-8564 and the wild type background strain were run in the sameassay as controls.

The results, provided in Tables 16-18 and shown in FIGS. 13A-13C, werestartling. All gene attenuation mutants, including original knockoutmutant GE-8564 (triangles), produced FAME in amounts greater than wildtype (circles) when cultured with nitrate as the sole nitrogen source onall days sampled (FIG. 13A, data provided in Table 16). However, whilethe original knockout strain GE-8564 (triangles) had a significantlyreduced rate of total organic carbon accumulation with respect to wildtype (FIG. 13B), in these conditions, the attenuated knockdownstrains—the “bash” strains and RNAi strain having reduced expression ofthe ZnCys-2845 gene—had rates of TOC accumulation close to or (forexample in the case of GE-13112 (represented as Xs)) essentiallyidentical to, wild type (FIG. 13B, data provided in Table 17).Remarkably, these ZnCys-2845 knockdown mutants demonstrated FAME to TOCratios that were significantly enhanced with respect to wild type (FIG.13C and Table 18), although not as high as the FAME to TOC ratios of theZnCys-2845 knockout mutant GE-8564, i.e., the carbon partitioning tolipid in these knockdown attenuation strains was intermediate betweenthat of wild type and the ZnCys-2845 knockout strain.

TABLE 16 FAME Productivity of ZnCys-2845 Knockdown Strains Compared toWild Type in Batch Assay with NO₃-Containing Culture Medium (mg/LCulture) BASH-2 BASH-3 BASH-12 RNAi-7 ZnCys-KO (GE-13108) (GE-13109)(GE-13112) (GE-13103) (GE-8564) Day WT % incr % incr % incr % incr %incr 3 159.22 279.72 75.68 260.14 233.36 233.36 40.64 233.36 46.56242.05 52.02 5 191.33 446.40 133.31 377.8 368.41 368.41 55.98 368.4192.55 360.89 88.67 7 270.37 599.06 121.57 431.41 460.69 460.69 27.96460.69 70.39 473.53 75.14

TABLE 17 TOC Productivity of ZnCys-2845 Knockdown Strains Compared toWild Type in Batch Assay with NO₃-Containing Culture Medium (mg/LCulture) BASH-2 BASH-3 BASH-12 RNAi-7 ZnCys-KO (GE-13108) (GE-13109)(GE-13112) (GE-13103) (GE-8564) Day WT % diff % diff % diff % diff %diff 3 642.4 608.1 −5.34 615.05 −4.26 627.2 −2.37 497.4 −22.57 281.5−56.18 5 920.75 827.9 −10.09 836.9 −9.11 913.95 −0.74 713.4 −22.52 408.8−55.01 7 1188 1044.5 −12.08 1044 −12.12 1175.5 −1.05 929.2 −21.78 558.15−53.18

TABLE 18 FAME/TOC Ratios of ZnCys-2845 Knockdown Strains Compared toWild Type in Batch Assay with NO₃-Containing Culture Medium BASH-2BASH-3 BASH-12 RNAi-7 ZnCys-KO WT-3730 (GE-13108) (GE-13109) (GE-13112)(GE-13103) (GE-8564) Day s.d. s.d. s.d. s.d. s.d. s.d. 3 0.2478 0.00920.4599 0.0090 0.4229 0.0096 0.3570 0.0043 0.4690 0.0146 0.8608 0.0334 50.2078 0.0012 0.5391 0.0059 0.4514 0.0025 0.3263 0.0106 0.5161 0.02300.8824 0.0393 7 0.2276 0.0012 0.5735 0.0051 0.4132 0.0036 0.2942 0.00330.4959 0.0069 0.8491 0.0593

FIG. 14A provides a diagram of the ZnCys-2845 gene and FIG. 14B providesa graph showing normalized ZnCys-2845 RNA levels in cultured strainshaving insertional BASH mutations (“basher” strains GE-13109 andGE-13112), the RNAi construct (ZnCys-2845 RNAi strain GE-13103), or theknockout (KO) mutation (ZnCys-2845 knockout mutant GE-8564) asquantitated by PCR using the methods provided in Example 7. The ZnCysBASH-3 strain GE-13109 demonstrated an approximately 20% reduction inZnCys-2845 transcript level, the ZnCys BASH-12 strain GE-13112demonstrated an approximately 50% reduction in ZnCys-2845 transcriptlevel, and the ZnCys-2845 RNAi isolate (GE-13103) demonstrated anapproximately 70% reduction in ZnCys-2845 transcript level. FIG. 14Cprovides a graph of the FAME/TOC ratio and TOC productivity of eachstrain based on a batch assay in nitrate-only medium as described above,except that in the assay of FIG. 14C, the ZnCys-2845 knockout strainGE-8564) was not precultured in the presence of ammonium but innitrate-only medium. As summarized in FIG. 14C, in batch growth with nonitrate, all three ZnCys-2845 gene attenuation lines exhibited increasesin carbon partitioning to lipid evident at FAME/TOC ratios (see alsoTable 18) that were intermediate between wild type and ZnCys knockout(strain GE-8564) FAME/TOC ratios. TOC accumulation in the knockdownmutants were nearly equivalent to wild type (the ZnCys RNAi-7 strainGE-13103 having the greatest impairment of only about 20%), showing asubstantial improvement over the reduction shown in the ZnCys-2845knockout mutant which demonstrates an approximately 85% reduction inaverage daily TOC productivity (FIG. 14C). The daily FAME and TOC valuesof the batch assay from which the data of FIG. 14C is derived areprovided in the graphs of FIGS. 15A and 15B.

Example 10 ZNCYS-2845 Knockdown Mutants in the Semi-ContinuousProductivity Assay

ZnCys-2845 RNAi strain GE-13103, BASH2 strain GE-13108, BASH3 strainGE-13109, and BASH12 strain GE-13112 were then assayed in thesemi-continuous productivity assay described in Example 6, except thatin this case the assay medium, PM074, included nitrate as the solenitrogen source and the knockdown strains were pre-cultured in PM124medium that included 5 mM ammonium in addition to 8.8 mM nitrate. Forthe GE-13103 ZnCys-2845 RNAi strain, productivity was assayed in twoways: a first set of semi-continuous assay cultures was inoculated usingstarter cultures that included the PM074 nitrate-only culture medium,and a second set of GE-13103 semi-continuous assay cultures wasinoculated using starter cultures that included 5 mM ammonium inaddition to 8.8 mM nitrate (PM124 medium).

The starter cultures were used to inoculate 225 cm² rectangular tissueculture flasks, each of which contained a final total volume of 550 mlof culture after inoculation. The cultures were inoculated so that each550 ml culture had an initial OD₇₃₀ of 0.9. A typical inoculum volumewas approximately 200 ml of scale-up culture that was added toapproximately 350 ml of assay culture medium, which was PM074(nitrate-only medium). Cultures were diluted daily at mid-day, when thelight intensity was at its peak, by removing 30% of the volume (165 mls)and replacing it with the same volume of the assay medium (PM074) plusan additional 10 ml of deionized water to make up for evaporation(included in the make-up medium). Thus, assay cultures inoculated fromscale-up ZnCys-2845 RNAi cultures that included 5 mM ammonium in theculture medium (PM124 medium) started out with a significant amount ofammonium (e.g., about 2 mM ammonium or less) that progressively declinedand was diluted out further during the course of the assay.Semi-continuous assays were typically run for 10-14 days. Daily lipidand biomass productivities were only calculated for cultures that hadreached steady state (where the increase in growth was equal to thedilution factor for the assay).

During the course of the semi-continuous assay, daily 30% dilutions werewith nitrate-only medium (PM074) for all cultures. In these assays, muchmore lipid was produced on a daily basis by the GE-13103 RNAi knockdowncells scaled up in nitrate-only medium in the semi-continuous assay(filled-in circles, FIG. 16A) as compared with wild type cells, whichwere in nitrogen replete conditions (diamonds). The amount of lipidproduced on a daily basis by the GE-13103 strain was even higher whenthe scale-up culture medium included ammonium in addition to nitrate(open circles in FIG. 16A). BASH2 strain GE-13108 (Xs), BASH3 strainGE-13109 (triangles), and BASH12 strain GE-13112 (squares) also producedconsiderably more FAME in the semi-continuous assay than did the wildtype strain.

FIG. 16B provides the daily amount of FAME produced by the knockdownstrains in the semi-continuous assay that included nitrate as the solenitrogen source in the culture medium (PM074 medium). The knockdownstrains, which included GE-13108 (5′ Bash2), GE-13109 (5′ Bash3),GE-13112 (3′ Bash12), and GE-13103 (RNAi-7) were pre-cultured in nitrateplus ammonium medium PM124. The RNAi knockdown strain GE-13103 was alsoassayed after being pre-cultured in nitrate-only medium (PM074),alongside wild type strain WT-3730 pre-cultured in nitrate-only medium(PM074) (which is a nitrogen replete medium for the wild type strain).Knockout strain GE-8564 was cultured separately in nitrate-only (PM074)medium as the culture medium used in the semi-continuous assay. Thetable of FIG. 16B demonstrates that all of the knockdown strains hadhigher productivities than the wild type strain when cultured in thesemi-continuous assay with regular dilution using a culture medium inwhich nitrate was substantially the sole nitrogen source (PM074). Inthis assay, knockdown strain GE-13112 (BASH12), demonstrated productionof an average daily amount of FAME that was 83% greater than wild type,and knockdown strain GE-13109 (BASH3), demonstrated production of anaverage daily amount of FAME that was 81% greater than wild type onnitrate. Knockdown strain GE-13108 (BASH2), demonstrated production ofan average daily amount of FAME that was 88% greater than wild typediluted with the same culture medium (PM074) over the course of theassay. Thus, all of the insertional knockdown mutants targetingnon-coding regions of the ZnCys-2845 gene demonstrated substantialincreases in areal FAME productivity of at least 70% higher (andapproximately 80%-90% higher), than wild type cells in nitrate-onlyculture medium, with only minimal TOC productivity decreases ofapproximately 5-15% in the GE-13108 (BASH2), GE-13112 (BASH12), andRNAi-7 GE-13103 strains compared to the wild type strain (FIG. 16C). TheRNAi-7 strain GE-13103 pre-cultured in nitrate-only medium produced onaverage is 107% more FAME on a daily basis than wild type cultured underthe same conditions. The RNAi-7 strain GE-13103 pre-cultured in a mediumthat included both ammonium plus nitrate produced on average is 122%more FAME on a daily basis than wild type cultured under the sameconditions. Thus, the GE-13103 gene attenuation mutant produced at leasttwice as much lipid as wild type in a semi-continuous assay in which thecultures were regularly diluted with nitrate-only medium, regardless ofthe nitrogen source in the pre-culture medium. The knockout mutant,GE-8564, also produced somewhat more FAME than wild type in the assay,although the increase was not as great as for the knockdown mutants(approximately 40% greater than when both were cultured in nitrate-onlymedium). The amount of FAME produced by knockout mutant GE-8564 culturedin nitrate-only medium fell off drastically beginning at about day 6 ofthe culture, reflecting large losses in biomass (Table 20).

These improvements in FAME productivity by the knockdown strains arepresented as a percentage increase over wild type, averaged over theduration of the culture, in Table 19. All of the knockdown strains(GE-13103, GE-13108, GE-13109, and GE13112) had increases in FAMEproductivity (i.e., g/m²/day) with respect to wild type over the courseof the culture, ranging from 81% to 122% over the course of the entireculture, with even greater productivity increases seen in the first fourdays of culturing, ranging from 100% (i.e., twice the wild typeproductivity) to 160%. GE-13103, the RNAi knockdown strain, had thelargest productivity increase with respect to wild type over the courseof the semi-continuous culture, approximately 100% improvement (whenpre-cultured in PM074) and approximately 120% improvement (whenpre-cultured in PM124).

TABLE 19 FAME Productivity of Knockdown and Knockout Strains (g/m2/day)Day 1-Day 4 Day 8-Day 11 Day 1-Day 11 % % % Strain s.d. impr s.d. imprimpr WT-3730 2.37 0.11 — 2.41 0.08 — 2.43 — GE-13112 4.75 0.20 100% 4.140.10  72% 4.44  83% (BASH-12) GE-13109 4.89 0.16 107% 3.90 0.13  62%4.39  81% (BASH-4) GE-13108 6.15 0.43 160% 2.84 0.46  18% 4.55  88%(BASH-3) GE-13103 5.45 0.17 130% 4.39 0.19  82% 4.95 104% (RNAi-7)(pre-cultured in NO3) GE-13103 5.83 0.32 146% 4.82 0.26 100% 5.40 122%(RNAi-7) (pre-cultured in NH4 + NO3) GE-8564 2.98 0.20  26% 3.14 0.12 30% 3.22  33% (ZnCys-KO) Urea medium GE-8564 5.80 0.84 145% 1.16 0.43−52% 3.39  40% (ZnCys-KO) Nitrate medium

The amount of TOC accumulated on a daily basis by the knockdown strainswas only slightly to modestly less than the TOC accumulated by wild typein knockdown cultures, GE-13109 (5′ Bash-3), and GE13112 (3′ Bash-12)although it was significantly lower in GE-13108 (5′ Bash-2) and knockoutstrain GE-8564 cultured in nitrate-only medium (FIG. 16C and Table 20).Nevertheless, the TOC productivity in the RNAi knockdown strain(GE-13103) that exhibited an approximately 100% increase in FAMEproductivity over 11 days (and approximately 120% increased whenprecultured with ammonium) was only about 18% reduced with respect towild type, and the TOC productivities of BASH-12 and BASH-4 knockdownmutant strains GE-13112 and GE-13109 (that demonstrated increases of atleast 80% in FAME productivity over eleven days) were decreased by only5% or less.

TABLE 20 Daily Average TOC Productivity of Knockdown and KnockoutStrains Strain g/m²/day s.d. % diff WT 9.50 0.30  0% GE-13112 (BASH-12)9.43 0.60  −1% GE-13109 (BASH-3) 9.06 0.56  −5% GE-13108 (BASH-2) 6.332.32 −33% GE-13103 (RNAi-7) 7.75 0.87 −18% (pre-cultured in NO3)GE-13103 (RNAi-7) 8.27 1.09 −13% (pre-cultured in NH4 + NO3) GE-8564(ZnCys-KO) 8.86 0.26 −7% Cultured in Urea GE-8564 (ZnCys-KO) 4.68 2.88−51% Cultured in NO3

The ZnCys-2845 knockdown and knockout cultures all demonstratedincreased FAME to TOC ratios as compared to wild type (solid diamonds)in the semicontinuous assay in nitrate medium (FIG. 16D and Table 21).When scaled up in nitrate only medium, the RNAi knockdown strainGE-13103 (closed circles) demonstrated a greater than 100% increase,approximately a 150% increase, in FAME/TOC ratio with respect to wildtype and the same GE-13103 strain scaled up in nitrate plus ammoniummedium (open circles) demonstrated an 153% increase in their FAME to TOCratio in the semi-continuous productivity assay (Table 21).

TABLE 21 FAME/TOC Ratios of Knockdown and Knockout Strains Strainfame/toc s.d. % impr WT-3730 0.26 0.02  0% GE-13112 (BASH-12) 0.47 0.01 82% GE-13109 (BASH-3) 0.48 0.02  87% GE-13108 (BASH-2) 0.73 0.05 180%RNAi-7 0.64 0.02 147% (precultured in NO3) RNAi-7 0.66 0.04 153%(precultured in NO3 + NH4) GE-8564 0.36 0.03  41% (ZnCys-KO) Cultured inUrea GE-8564 0.69 0.11 168% (ZnCy s-KO) Cultured in NO3

These genetically engineered knockdown cells were able to partition moreof their carbon to lipid than wild type (FIG. 16D). The increasedFAME/TOC ratios were particularly notable in the ZnCys RNAi attenuationstrain GE13103, as it had only modest reductions in TOC (between about15% and about 20%, Table 20) coupled with increased FAME with respect towild type throughout the assay (greater than 100% increase, anapproximately 120% increase, Table 19).

Graphs of volumetric FAME and TOC productivities of wild type, Cas9Editor line GE-6791, and ZnCys-2845 knockdown lines GE-13112 (BASH-12A),GE-13109 (BASH-3A), and GE-13108 (BASH-2A) assayed in a separatesemicontinuous assay using nitrate-only medium are provided in FIGS. 17Aand 17B (data provided in Table 22 and Table 23), and the average areal(g/m²/day) TOC and FAME productivities of the wild type strain and Cas9editor line (as controls) and the BASH-3, BASH-12, and RNAi mutants (allpre-cultured in nitrate-only medium) in this assay are summarized in thegraph of FIG. 18, where it can be seen that the RNAi strain has thehighest FAME productivity of the tested mutants.

TABLE 22 Average Daily FAME Productivity of Knockdown Strains inSemi-Continuous Assay Using Nitrate-only Medium AV DAILY FAME %PRODUCTIVTY INCREASE STRAIN (sd) FROM WT WT 2.42 0 (0.13) ZnCys-BASH-124.19 73.1 (0.25) ZnCys-BASH-3 4.48 85.1 (0.35) ZnCys-RNAi-7 4.88 101.7(0.44) Ng-Cas9+ 2.53 4.5 (0.10)

TABLE 23 Average Daily FAME Productivity of Knockdown Strains inSemi-continuous Assay Using Nitrate-only Medium AV DAILY TOC %PRODUCTIVITY DECREASE STRAIN (sd) FROM WT WT 9.96~(0.47) 0 ZnCys-BASH-129.48~(0.42) 4.8 ZnCys-BASH-3 9.04~(0.40) 9.2 ZnCys-RNAi-7 8.09~(0.58)18.8 Ng-Cas9+ 9.80~(0.45) 1.6

The increases in FAME/TOC were significantly less at the outset of theculture period in the ZnCys RNAi attenuation cultures that had beenpre-cultured in a medium containing a mixture of nitrate and ammoniumthan in the ZnCys RNAi attenuation cultures that had been pre-culturedin a medium containing only nitrate (FIG. 16D). Thus it appeared thatstrains pre-cultured in nitrate plus ammonium media included reducednitrogen (ammonium) from the pre-culture that was introduced into theassay cultures, and this residual ammonium repressed lipid biosynthesisto some degree. This effect disappeared by the fifth day of the assay(see FIG. 16A, open circles (RNAi strain precultured with ammonium inthe medium) versus solid circles (RNAi strain precultured with onlynitrate in the medium)), by which time the rate of production of lipidby the ZnCys RNAi attenuation strain did not significantly differbetween cultures that had been inoculated with a seed culture thatincluded ammonium and nitrate and cultures that had been inoculated witha seed culture that included only nitrate as a nitrogen source. At thispoint presumably the cultures that had been pre-cultured in medium thatincluded ammonium ran out of their reduced nitrogen source and inducedlipid biosynthesis to approximately the same degree as the cultures thathad not been pre-cultured in an ammonium-containing medium. Thisinterpretation was supported by analysis of the nitrogen present in thecultures. For total nitrogen (TN) analysis of cell pellets, 10 mlculture samples were spun down, the media removed from the pellets, andeach pellet was resuspended in 1 ml nanopure H₂O, which was thentransferred to a 22 ml vial, to which 19 ml of nanopure H₂O was added.Total nitrogen analysis was performed using a ShimadzuTOC-V_(CSH)/VN_(M-1) analyzer. FIG. 19 shows that the amount of totalnitrogen in the cell pellets was significantly higher in the GE-13103cultures that had been inoculated with a pre-culture that includedammonium in the medium (open circles) than in in the cultures that hadbeen inoculated with a pre-culture that included only nitrate (NO₃)(e.g., closed circles). Thus it appeared that the ZnCys RNAi attenuationcells, while able to utilize nitrate for growth (as evidenced bycontinued TOC accumulation, e.g., FIG. 16C), still induced lipidbiosynthesis as long as ammonium was present at low concentrations, forexample, of less than about 2 mM or less than about 1.5 mM.

The relationship between the amount of ammonium present in theZnCys-2845 RNAi strain GE-13103 cultures during semi-continuous assayswas investigated in semi-continuous productivity assays performed asdescribed above in which daily samples were analyzed for nitrogencontent of the whole culture (culture medium plus cells) as well as FAMEcontent as described in the examples above.

FIG. 20 shows the amount of FAME and nitrogen present in the culture onsuccessive days of semi-continuous culture graphically. Whole culturetotal nitrogen (TN) was determined by removing a 2 ml sample of theculture to a 22 ml vial, to which 18 ml of nanopure H₂O was added, andanalyzing the sample using a Shimadzu TOC-V_(CSH)/VN_(M-1) analyzer. Theamount of nitrate that could be accounted for in the PM074 medium wassubtracted from the total nitrogen of the sample to arrive at the amountof nitrogen present as ammonium indicated in FIG. 19. Because theammonium present in the PM124 starter culture was progressively dilutedout of the cultures that were inoculated with PM124 (NH₄+NO₃) startercultures, it can be seen that for this sample, FAME production (opendiamonds) rises as ammonium concentration (solid diamonds) falls.Ammonium levels in the culture below about 2.5 mM, and especially belowabout 2 mM, appeared to result in induction of FAME production in theattenuated RNAi strain (open diamonds).

Example 11 Relationship of Productivity of ZNCYS-2845 AttenuationMutants to Available NH₄ Concentration

The relationship between nitrogen availability and FAME productivity inthe ZnCys-2845 RNAi strain GE-13103 was further investigated in asemi-continuous productivity assay as described in Example 10 exceptthat the semi-continuous assay was performed in three separate culturemedia in which the concentration of ammonium was held constant at threedifferent levels. Wild type Nannochloropsis gaditana (WT-3730) was alsoincluded in the assay, where the wild type strain was cultured in thestandard PM074 medium that included no ammonium (but included 8.8 mMnitrate as the sole source of nitrogen).

In this experiment, starter cultures that included culture mediumcontaining either 0.5 mM, 1.0 mM, or 2.5 mM ammonium in addition to 8.8mM nitrate were used to inoculate assay flasks that included culturemedia that included the corresponding amount of ammonium (in addition to8.8 mM nitrate). After reaching steady state the cultures were dilutedback daily with the ammonium-supplemented media, such that one set oftriplicate cultures in which the assay medium included 0.5 mM ammoniumwas inoculated from a seed culture that included 0.5 mM ammonium and wasdiluted daily with a medium containing 0.5 mM ammonium throughout theassay, another set of triplicate cultures was inoculated from a seedculture that included 1.0 mM ammonium and included 1.0 mM throughout theassay, and a third set of triplicate cultures was inoculated from a seedculture that included 2.5 mM ammonium and included 2.5 mM ammoniumthroughout the assay. In each case, the medium was PM074 that includes8.8 mM nitrate as the sole source of nitrogen that can be used by themicroorganisms, supplemented with the appropriate amount of NH₄Cl aswell as with 5 mM Hepes, pH 7.5. The results can be seen in Tables22-24. All samples were assayed in triplicate, and provided values arethe average of the three cultures.

FIG. 21A shows the amount of FAME present in the culture on successivedays of semicontinuous culture for cultures held at 0.5 mM, 1.0 mM, and2.5 mM ammonium (solid diamond and triangles, representing RNAisymbols). It can be clearly seen that reducing the ammoniumconcentration of the culture from 2.5 mM (squares) to 1.0 mM (triangles)increases FAME productivity, which is increased even further when theammonium concentration is maintained at 0.5 mM (Xs) (see also Table 24).

TABLE 24 Daily FAME Content (mg/L) of Cultures: Average of TriplicateFAME Values (sd) Strain Day1 Day2 Day3 Day4 Day5 Day6 Day7 Day8 Day9Day10 WE-3730 44.3 46.31 48.63 48.27 45.91 44.35 45.73 46.48 45.07 41.15(0.32) (1.53) (1.87) (0.76) (1.66) (1.47) (0.16) (0.81) (0.91) (5.94)GE-13103 35.9 35.5 39.0 35.3 32.5 29.7 35.1 42.3 57.8 41.2 2.5 mM NH4Cl(2.92) 3.24 0.16 0.46 3.36 4.15 2.01 5.09 0.80 3.17 GE-13103 60.0 58.358.8 55.3 51.7 48.2 52.5 57.6 60.9 54.5 1.0 mM NH4Cl (1.85) (1.20)94.290 (0.79) (5.83) (5.75) (6.97) (1.92) (1.11) (1.41) GE-13103 83.585.8 87.4 84.4 81.1 75.4 73.9 78.4 83.6 76.9 0.5 mM NH4Cl (0.86) (0.290(0.980 (0.550 (5.130 (3.37) (3.80) (3.35) (4.60) (3.11)

The FAME productivity is provided in the table of FIG. 21B. The FAMEproductivity of the GE13103 knockdown strain in 2.5 mM NH₄ medium isreduced by about 15% with respect to wild type FAME productivity innitrate-only medium (which does not induce lipid production in the wildtype strain). At lower ammonium concentrations however, the knockdownmutant shows greater FAME productivity over the course of the assay thandoes the wild type strain. For example, in culture medium in which theammonium concentration is 1 mM, the knockdown mutant strain demonstratesan increased average daily FAME productivity of 22%, while at 0.5 mMammonium, GE-13103 demonstrates an increased average daily FAMEproductivity of 77% with respect to the wild type strain, that is, theGE-13103 knockdown strain at very low ammonium concentration producesalmost twice as much FAME lipids as wild type.

Nevertheless, FIG. 21C shows that reducing the ammonium concentration ofthe culture medium below 2.5 mM NH₄ does not have a major effect on TOCaccumulation by the GE13103 knockdown mutant (Table 25).

TABLE 25 Daily TOC Content (g/m²/day): Average of Triplicate Values (sd)Strain Day1 Day2 Day3 Day4 Day5 Day6 Day7 Day8 Day9 Day10 Day 11 WT-3730179.3 177.35 181.7 181.57 172.43 173.7 172.13 171.67 174.1 185 189.47(7.56) (3.04) (1.56) (7.38) (6.09) (5.36) (3.50) (4.44) (4.36) (2.19)(4.35) GE-13103 137.7 131.1 132.5 123.2 118.6 125.2 127.9 134.9 143.2153.0 167.5 2.5 mM NH4 (5.59) (6.92) (1.70) (10.63) (13.35) (13.36)(11.15) (5.61) (4.55) (7.74) (12.62) GE-13103 155.2 155.7 152.2 153.0147.3 163.2 151.2 155.3 162.8 170.0 176.1 1.0 mM NH4 (10.53) (14.08)(12.84) (15.22) (16.67) (8.20) (19.97) (15.51) (13.06) (11.60) (10.77)GE-13103 164.4 167.7 169.1 166.2 160.2 159.7 155.8 160.2 164.3 169.1172.4 0.5 mM NH4 (4.95) (4.74) (6.86) (5.11) 7.06) (6.33) (7.68) (5.65)(6.22) (1.99) (7.35)

For example, the average daily TOC productivity of the knockdown mutantstrain cultured in 0.5 mM ammonium was essentially identical to that ofwild type cultured under nitrogen replete (nitrate only) conditions(FIG. 21D). Thus, the GE-13103 knockdown mutant demonstrated at least75% more lipid productivity while demonstrating no reduction in biomassproductivity with respect to wild type cells in nitrogen repleteconditions over a period of at least 10 days of culturing. As shown inFIG. 21F, cell counts, as determined by flow cytometry, remainedreasonably consistent for a given ammonium concentration throughout theassay, indicating that the cells were actively dividing throughout thesemi-continuous assay under all conditions, including conditions inwhich the low-ammonium cultures were induced for lipid biosynthesis, asindicated by the elevated FAME/TOC ratios of the 1 mM ammonium and 0.5mM ammonium-containing cultures (as demonstrated in FIG. 21E).

The FAME to TOC ratio of the GE-13103 knockdown mutant cultured inmedium having varying ammonium concentrations is shown in FIG. 21E. TheFAME to TOC ratio remains between about 0.3 and 0.4 when the ammoniumconcentration is between about 1 mM and about 2.5 mM, but increasesfurther when the ammonium concentration drops from about 1.0 mM to about0.5 mM, remaining close to 0.5 throughout the assay using 0.5 mMammonium in the medium, for example well within the range of betweenabout 4.0 and about 6.0, and within the region of between about 4.5 andabout 5.5 (see Table 26).

TABLE 26 FAME/TOC Ratios: Average of Triplicate FAME/TOC Values (sd)Strain Day1 Day2 Day3 Day4 Day5 Day6 Day7 Day8 Day9 Day10 WT-3730 0.20.3 0.27 0.27 0.27 0.26 0.27 0.27 0.26 0.22 (0.01) (0.01) (0.01) (0.01)(0.00) (0.00) (0.01) (0.01) (0.00) (0.03) GE-13103 0.3 0.3 0.3 0.3 0.30.2 0.3 0.3 0.4 0.3 2.5 mM NH4Cl (0.01) (0.01) (0.00) (0.00) (0.01)(0.01) (0.01) (0.03) (0.01) (0.01) GE-13103 0.4 0.4 0.4 0.3 0.4 0.3 0.30.4 0.4 0.3 1.0 mM NH4Cl (0.00) (0.00) (0.01) (0.01) (0.00) (0.00)(0.00) (0.03) (0.03) (0.01) GE-13103 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.50.5 0.5 mM NH4Cl (0.02) (0.01) (0.01) (0.01) (0.01) (0.02) (0.02) (0.00)(0.01) (0.01)

Thus, the strains obtained by attenuating expression of a gene asprovided here that regulates lipid biosynthesis are able to activelydivide while producing considerably more lipid than wild type. Theability to sustain elevated levels of lipid production without a declinein TOC accumulation throughout the assay (FIGS. 22A-22E), indicates themutants provided herein can provide sustained high-level lipidproduction such as in continuous and semi-continuous cultures.

Example 12 Analysis of Protein, Carbohydrate, and Lipid Content of ZnCysMutants

In the above experiments (e.g., Example 4), FAME and TOC productivitiesof knockout mutant strain GE-8564 were found to be essentially equal tothose of the wild type strain when both were cultured in the presence ofammonium (FIGS. 8A-8C), suggesting that a bottleneck in nitrateassimilation led to the marked phenotypes of increased lipid productionthat were observed only when nitrate was used as the sole nitrogensource. Knockdown mutants of ZnCys-2845 were observed to exhibitsubstantial increases in FAME productivity (Table 16 and FIG. 13A aswell as FIGS. 16A and 16B) with minimal TOC decreases of from about 1%to about 33% (Table 17 and FIG. 13B; FIG. 16C). FAME and TOCproductivities for a semi-continuous assay that included wild-type,ZnCys-2845 BASH-3, ZnCys-2845 BASH-12, and ZnCys-2845 RNAi strainGE-13103 are shown in the graphs of FIGS. 17A and 17B, respectively.ZnCys BASH-3, ZnCys BASH-12, and ZnCys RNAi all exhibited substantialincreases in aerial FAME productivity (up to 103% for ZnCys RNAi-7) withonly minimal TOC decreases of approximately 5-15% compared to the wildtype strain and the Cas9 progenitor line (FIG. 18). To determine howcarbon was allocated to major categories of biomolecules, the strainswere grown in the semi-continuous assay system as described in Example10, where the PM074 dilution medium included nitrate as the solenitrogen source. In this assay the RNAi line demonstrates increased FAMEproductivity and the knockout line is unable to maintain growth (FIGS.22A-E). The strains from these cultures were assessed for carbohydrate,lipid, and protein, which together accounted for about 75% of TOC.

For HPLC analysis of lipids, 2 ml samples of each culture were spun downat maximum speed for 5 minutes, the supernatants were removed, andpellets were re-suspended in 400 μL of H₂O. The cell suspensions(approximately 500 μL) were transferred to 4 ml glass vials with Teflonlined caps. 500 μL of glass beads (212-300 μm diameter) were added toeach of the cell suspensions, after which 50 μL of 50% H₂SO₄ and 100 μLof 5M NaCl were added. Bead beating was performed for 5 minutes at 1krpm, then 2 ml of hexane was added to each sample, and bead beating wasrepeated for 5 minutes at 1 krpm. The samples were loaded onto amulti-tube vortexer and shaken for 30 minutes at 1 krpm, and thenvortexed for 30 seconds at 2.5 krpm. 500 μL of the organic layer wastransferred to an HPLC vial, and 50 μL of internal standard solution (1mg/ml 6-ketocholestanol in toluene) was added to each vial. Standardswere from NuCheck, Sigma-Aldrich, or Supelco. The vials were capped andvortexed briefly (5 seconds at 2.5 krpm) prior to HPLC analysis. TheHPLC was run at a flow rate of 2 ml/minute on a Chromegasphere SI-60 150mm×4.6 mm×10 μm column (ES Industries), with a column compartment set at40° C. The injection volume was 25 μL with a draw and eject speed of 200μL/minute. Eluent A was hexane and Eluent B was an 80:10:10:1 mixture ofhexane, isopropanol, ethyl acetate, and 10% formic acid in isopropanol,run as a gradient program as follows: 2% B at 0.0 min; 2% B at 1.0 min;35% B at 8.0 min; 98% B at 8.5 min; 98% B at 11.5 min; 2% B at 11.6 min;stop time: 11.6 minutes; 5 minutes post time. The detector was ELSD at30° C. and 3.5 bar N2, with a gain of 5.

Total carbohydrate analysis was conducted on ˜0.7 mg TOC equivalent ofcell culture concentrated to 0.5 ml in phosphate buffered saline (PBS)after three centrifugations followed by washing with PBS. Acidhydrolysis was used to convert carbohydrates to their constituentmonomers by the addition of 0.5 ml deionized H₂O and 1 ml 6 N HCl andU-¹³C-glucose and -galactose as internal standards at a finalconcentration of 50 μg/ml each. Samples were heated at 105° C. for onehour in glass vials with PTFE-lined capped. One hundred μl aliquots ofthe room temperature cooled, 3,000 g centrifuged (1 min) samples weredried in an EZ-2 Genevac (Stoneridge, N.Y.) and derivatized withMSTFA/TMCS and analyzed by GC-MS according to Ruiz-Matute et al. (2011)J. Chromatogr B Analyt Technol Biomed Life Sci 879: 1226-1240. Internal¹³C labeled standards were used to quantify the concentration of themajor carbohydrate monomers, glucose and galactose, and estimate theconcentration of less abundant sugars (arabinose, rhamnose, xylose, andmannose). These were summed to yield a total saccharide concentration inug/ml which was converted to the carbon content of total carbohydratesby a multiplication factor of 0.45 (i.e., ˜45% of carbohydrate mass isrepresented by carbon. This value was divided by the amount of TOCdetected in an identical aliquot of concentrated cell culture toestimate the percent of carbon allocated to carbohydrate.

Total amino acid analysis was conducted by derivatization of whole aminoacid hydrolysate to propoxycarbonyl propyl esters using a modifiedmethod according to the EZ:faast kit from Phenomenex (Torrance, Calif.).Briefly, to 0.5 ml concentrated cells (as described for carbohydrateanalysis above) 800 μl of 6 N HCl containing 200 μl/ml thioglycolicacid, 10 ul of β-mercaptoethanol, and 200 ul of 2 mM norvaline (internalstandard) were added and the vortexed sample was incubated at 110° C.for 24 h. Samples cooled to room temperature were centrifuged at 1,500 gfor 1 minute and a 50 μl aliquot was transferred to a fresh 2 ml GCvial. Aliquots were derivatized and analyzed by GC-MS according to theEZ-faast manual and (8). This method allowed for the quantification ofAla, Gly, Val, Leu, Ile, Pro, Asp+Asn, Met, Glu+Gln, Phe, Lys, Tyr, andCys; Trp, Thr, Ser, Arg, and His were excluded. Volumetricconcentrations of each detected hydrolyzed amino acid was converted tothe carbon content present in that amount. These values were summed toand normalized to TOC as described for total carbohydrates above to givean estimate of carbon allocated to protein.

The results are seen in FIG. 23, where it can be seen that bothattenuated ZnCys mutants ZnCys-BASH-12 and ZnCys RNAi had decreases ofapproximately 45-50% in protein compared to the wild type strain,accompanying an approximately 90-125% increase in lipids in the strains.Consistently, the ZnCys knockout strain were observed to have thehighest C:N ratios while ZnCys RNAi displayed more intermediate levels(FIG. 22C), suggesting there may be a threshold C:N value that maximizeslipid productivity. The ZnCys knockout strain appears to be beyond thatthreshold, partitioning so much carbon into lipid that overall biomassand lipid productivity are negatively affected. In contrast, in this setof gene attenuation mutants, the ZnCys RNAi appears to have the optimalC:N value for lipid productivity in the range of about 10-15.

TABLE 27 Protein, Carbohydrate, and Lipid (FAME) % Composition of WildType and ZnCys Knockdown Strains Change Change Change Change STRAINProtein from wt Carb from wt FAME from wt Other from wt WT 40.2 0 11.2 019.6 0 29.1 0 (0.55) (0.50) (0.32) (0.27) ZnCys-BASH- 22.5 −44% 12.7+13% 37.6  +92% 27.2 −6.5% 12 (0.70) (0.12) (2.19) (2.94) ZnCys-RNAi-720.1 −50% 12.7 +13% 42.7 +118% 24.9  −14% (2.43) (0.70) (4.73) (1.59)

BASH-12 strain GE-1112 allocated approximately 38% of its carbon to FAMElipids, and approximately 22% of its carbon to protein, while RNAistrain GE-13103 allocated approximately 43% of its carbon to lipid, andapproximately 20% of its carbon to protein. This is distinguished fromwild type cells in nitrate-only medium that allocate approximately 20%of carbon to lipid, and approximately 40% of carbon to protein. (In bothmutants and wild type cells, approximately 10-15% of carbon is allocatedto carbohydrates.) Thus both ZnCys gene attenuation (“knockdown”)mutants increased carbon allocation to lipid by 90-120% (doubling lipidproductivity with respect to wild type) largely at the expense ofallocation of carbon to protein, which dropped by about 40-50% withrespect to the carbon allocation to protein in wild type cells culturedunder the same conditions.

Example 13 Transcriptomic Analysis of the ZNCYS-2845 Knockout andKnockdown Mutants

The ability of ZnCys-2845 knockout strain GE-8564 to accumulate FAME andTOC at levels essentially identical to wild type cells when the culturemedium was supplemented with ammonium (Tables 7-9, FIG. 8), indicatedthe mutant was impaired in nitrate assimilation. To further investigatenitrogen assimilation in these mutants, steady-state mRNA levels of keyN-assimilation genes by qRT-PCR were determined to gain a betterunderstanding of N-deficiency in the mutants under induced (nitrate-onlymedium) and non-induced (ammonium supplementation) conditions.

A nitrate reductase mutant was engineered using the same Cas9 Editorline described in Example 2. Briefly, a guide RNA was designed havingthe target sequence of a portion of the coding region of the N. gaditananitrate reductase gene Naga_100699 g1. The guide RNA (having targetsequence SEQ ID NO:193) was synthesized as disclosed in Example 3, andtransformed into the Cas9 editor line along with the donor fragment (SEQID NO:44) as described in Example 2. The resulting nitrate reductaseknockout strain (NR-KO) served as a control for the inability toassimilate nitrate, as a functional nitrate reductase enzyme isnecessary to assimilate nitrogen when nitrate is the sole nitrogensource. Effectively, the NR-KO strain is under nitrogen starvation whencultured in nitrate-only medium.

Steady-state mRNA levels of key N-assimilation genes were assessed byqRT-PCR to gain a better understanding of N-deficiency in the mutantsunder induced (NO₃ ⁻) and non-induced (NH₄ ⁺) conditions, where thenitrate reductase mutant (NR-KO) created by Cas9-mediated mutagenesiswas used as an N-starvation control under growth on NO₃ ⁻. When grown onmedium that included ammonium all strains shared similar gene expressionprofiles for the N-assimilation gene set, consistent with their wildtype phenotype with regard to biomass and FAME accumulation whencultured with ammonium-containing medium (FIG. 24, ammoniumtranscriptional profiles of the ZnCys knockout, the ZnCys RNAiknockdown, wild type, and the NR knockout shown in columns 2-5).

TABLE 28Primer Sequences for Transcripts Measured by Quantitative Real-Time PCRN. gaditana qRT-PCR sense primer/ Gene Description genome IDqRT-PCR antisense primer NAR1 Formate Nitrite Naga_100100g7GCCAACCTGCCAGTAAAATTC Transporter (SEQ ID NO: 153) AGAGCGGGATTCTGTTCTTG(SEQ ID NO: 154) Amt2 Ammonium Transporter Naga_100099g15AGAACGTGGGTAAGATGCAAC (SEQ ID NO: 155) ACCAGCCAAACCAGAGAAG(SEQ ID NO: 156) GS2 Glutamine Synthase Naga_100003g119GGCATACCTATTCATCCGCTAG (SEQ ID NO: 157) CAAATGACCAAGCACCAACTC(SEQ ID NO: 158) NAR2 Nitrite Transporter Naga_100046g36GCGAGGCATCTTGTGAATTG (NAR1) (SEQ ID NO: 159) ACGGAGTGTTCAAATCCCAG(SEQ ID NO: 160) GS1 Glutamine Synthase Naga_100056g25CATGGACTCATTCTCCTACGG (SEQ ID NO: 161) ATCCTCGAAATATCCGCACC(SEQ ID NO: 162) GOGAT1 Glutamate Synthase Naga_101084g2TGGATGCAAACGAGATGCTAG (SEQ ID NO: 163) AGGAAAGCGGGAATAGTGTG(SEQ ID NO: 164) GDH Glutamate Naga_100063g22 GGGACTCGTTGGAAGGTAAGDehydrogenase (SEQ ID NO: 165) CATTTCCACAAGTTTCTCCGC (SEQ ID NO: 166)GOGAT2 Glutamate Synthase Naga_100005g23 AAGGGAATGTCTTGGAACCG (plastid)(SEQ ID NO: 167) AGTGGGTAGACAGTGGAGAG (SEQ ID NO: 168) NRT2Nitrate high affinity Naga_100699g1 AGTGCTATGGAGTTTTGCGG Transporter(SEQ ID NO: 169) TTGGGATTTGGTCAAGGAGAG (SEQ ID NO: 170) NiRNitrite Reductase Naga_100852g1 GCCGATCCTTTCTTGCAAAC (SEQ ID NO: 171)AGCGTTCAATCAGGTCCAAG (SEQ ID NO: 172) NR Nitrate Reductase Naga_100699g1GCTATATTGGAGAATCCGGCG (SEQ ID NO: 173) GGGAACGTCAACAGTGATAGTG(SEQ ID NO: 174) Amt1 Ammonium Transporter Naga_100551g3g1CCTTCGGTGCCTATTTCGG AmtB-like protein (SEQ ID NO: 175)CATGTCGCTGGTATAGGATGC (SEQ ID NO: 176) UreT Urea active Naga_100311g2ATGGCAGTAGAAATGGACCC transporter-like (SEQ ID NO: 177) proteinAGTAAGAGAACGAAAAGGGCG (SEQ ID NO: 178) qRT-PCR Protein of UnknownNaga_100004g25 CTCTCCTATTGCTTTCCCTCG control Function (SEQ ID NO: 179)CTACCAACACCTCTACACTTCC (SEQ ID NO: 180)

However, when grown on nitrate as the sole nitrogen source, NR-KO showeda radically different expression profile from the ZnCys mutant lines(FIG. 24, column 1 compared with columns 6 & 7 showing transcriptionalprofiles of the ZnCys-2845 knockout and RNAi knockdown mutants).Consistent with previous reports on N-deprived N. gaditana (Radakovitzet al. 2012), a large number of genes involved in N-assimilation wereseverely upregulated in the NR-KO (shown in red color), including twoammonium transporters (AMT1 and AMT2), a glutamate synthase (GOGAT1), aNO₃ ⁻ transporter (NRT2) and nitrite reductase (NiR). Interestingly,this response was not observed for ZnCys mutants. In fact, geneexpression profiles for the ZnCys-2845 knockout and the ZnCys-2845 RNAiknockdown engineered mutants more closely resembled wild type underthese conditions, though NiR and NRT2 were significantly down regulatedin the ZnCys-2845 knockout with respect to wild type, thus offering apossible explanation to the N-deficiency of the cells (FIG. 22C).Analysis of protein levels by Western blotting showed that nitratereductase could not be detected in extracts of ZnCys-2845 knockoutstrain GE-8564, while a signal was detected in ZnCys-2845 RNAi knockdownstrain GE-13103 extracts as well as wild-type extracts (FIG. 25).Likewise, a very weak signal was observed for the nitrogen assimilationenzyme glutamine oxoglutarate aminotransferase (GOGAT1) in GE-8564,while it was more apparent for GE-13103.

Protein level changes in the plastid lipid biosynthetic machinery werealso assessed using specific peptide antibodies against ACCase and fattyacid synthesis (FAS) pathway components (FIG. 25). For antibodyproduction, two peptides (#1 and #2 in Table 29) were synthesized andinjected into rabbits. Terminal cysteines are shown for reference.

TABLE 29Peptide Sequences Used to Generate Antibodies Detecting Fatty AcidBiosynthesis Enzymes in N. gaditana N. gaditana Gene Descriptiongenome ID Peptide #1 Peptide #2 ACCase Acetyl-CoA Naga_100605g1C-FKFADTPDEESPLR C-AENFKEDPLRRDMR Carboxylase (SEQ ID NO: 181)(SEQ ID NO: 182) HAD 3-Hydroxy acyl Naga_100113g7 C-TANEPQFTGHFPERC-1DGVFRKPVVPGD ACP Dehydrase (SEQ ID NO: 183) (SEQ ID NO: 184) ENREnoyl-ACP Naga_101053g1 C-PEDVPEAVKTNKRY C-AIGGGEKGKKTFIE Reductase(SEQ ID NO: 185) (SEQ ID NO: 186) KAR β-Ketoacyl-ACP Naga_100037g12C-VAIKADMSKPEEVE C-SDMTEKLDLDG1KK Reductase (SEQ ID NO: 187)(SEQ ID NO: 188) KAS1 β-Ketoacyl-ACP Naga_100002g173 C-YMRGSKGQIYMKEKC-DAKPYFKDRKSAVR Synthase 1 (SEQ ID NO: 189) (SEQ ID NO: 190) KAS3β-Ketoacyl-ACP NG_scf10:19284.. MGKRSTASSTGLAY-C C-PPSIREVTPYKGKYSynthase 3 18979 (SEQ ID NO: 191) (SEQ ID NO: 192)

Compared to wild type, levels of these enzymes were not noticeablyhigher in ZnCys mutants, and in the case in NR-KO, ACCase and KAR1 werereduced. These data suggest that under N-replete conditions the plastidlipid biosynthetic machinery is already present at a capacity that iscapable of at least double the flux to fatty acid given the ˜100%increase in FAME productivity observed in ZnCys-2845 RNAi knockdownstrain GE-13103. This conclusion is consistent with transcriptionalchanges observed for N-deprived Nannochloropsis, where pathways involvedin providing carbon precursors to lipid biosynthesis appear to be moredifferentially expressed than “core” lipid biosynthetic pathways(Radakovitz et al 2012, Carpinelli et al 2014, Li et al 2014).

In order to gain further insight into the mechanisms that allow forZnCys-2845 attenuated lines to constitutively produce lipid and sustaingrowth, we analyzed the global transcriptional profiles of ZnCys-2845RNAi strain GE-13103 during steady-state growth conditions (e.g., FIGS.17A-17B). Using a 2-fold cut-off and FDR<0.05, 1118 genes were found tobe differentially expressed between ZnCys-RNAi-7 and wild type innitrate-only culture medium. Of these, 790 were up-regulated and 328down-regulated in the mutant. Analysis of the down-regulated gene setfor enriched gene ontology (GO) categories by “molecular function”,“biological process” or “cellular component” revealed that genesinvolved in photosynthesis and light harvesting were overrepresented inthe mutant with respect to the wild type (Table 30).

TABLE 30 Overrepresented Gene Ontology Categories Corresponding to Genesthat are Down-Regulated in ZnCys_RNAi-7 Over- FDR # genes # genes inrepresented adjusted Category Ontology^(†) GO Term DE^(††) categorypvalue pvalue^(†††) GO:0009765 BP photosynthesis, light 15 17 4.3E−117.4E−08 harvesting GO:0016168 MF chlorophyll binding 15 22 4.3E−082.4E−05 GO:0018298 BP protein-chromophore 15 22 4.3E−08 2.4E−05 linkageGO:0009523 CC photosystem II 18 39 1.3E−06 5.7E−04 GO:0003824 MFcatalytic activity 98 399 2.6E−05 8.9E−03 ^(†)BP, Biological process;CC, cellular component; MF, molecular function ^(††)DE, Differentiallyexpressed genes ^(†††)FDR, False Discovery Rate

The same analysis conducted on the up-regulated gene set revealed thatcomponents of protein synthesis were significantly enriched for in theattenuated ZnCys-2845 RNAi strain GE-13103 (Table 31). Considering thatour analysis of biomass composition indicated an approximately 45%decrease in total protein content in GE-13103 (FIG. 23), theup-regulation of translation machinery and down-regulation ofphotosynthetic apparatus is likely a response to that deficit.

TABLE 31 Overrepresented Gene Ontology (GO) Categories Corresponding toGenes that are Up-Regulated in ZnCys-2845 RNAi Strain GE-13103 Over- FDR# genes # genes in represented adjusted Category Ontology^(†) GO TermDE^(††) category pvalue pvalue^(†††) GO:0006412 BP translation 88 1751.9E−26 3.1E−23 GO:0005840 CC ribosome 77 160 5.1E−24 4.4E−21 GO:0003735MF structural constituent of 68 138 1.2E−22 6.5E−20 ribosome GO:0005622CC intracellular 85 226 1.1E−11 4.6E−09 GO:0005737 CC cytoplasm 70 1833.4E−07 1.2E−04 GO:0000166 MF nucleotide binding 175 525 5.5E−07 1.4E−04GO:0005524 MF ATP binding 206 636 5.6E−07 1.4E−04 GO:0005852 CCeukaryotic translation 10 11 2.2E−06 4.6E−04 initiation factor 3 complexGO:0003743 MF translation initiation 26 55 1.5E−05 2.8E−03 factoractivity GO:0005694 CC chromosome 12 18 2.3E−05 3.5E−03 GO:0006413 BPtranslational initiation 26 56 2.3E−05 3.5E−03 GO:0030529 CCRibonucleo-protein 34 109 2.9E−05 4.1E−03 complex GO:0006260 BP DNAreplication 20 37 1.1E−04 1.4E−02 GO:0015935 CC small ribosomal subunit8 13 2.0E−04 2.4E−02 GO:0005874 CC microtubule 17 30 4.3E−04 4.3E−02GO:0001731 BP formation of translation 5 5 4.9E−04 4.3E−02 preinitiationcomplex GO:0006446 BP regulation of 5 5 4.9E−04 4.3E−02 translationalinitiation GO:0016282 CC eukaryotic 43S 5 5 4.9E−04 4.3E−02preinitiation complex GO:0033290 CC eukaryotic 48S 5 5 4.9E−04 4.3E−02preinitiation complex GO:0051082 MF unfolded protein 14 28 5.4E−044.4E−02 binding GO:0007155 BP cell adhesion 8 10 5.5E−04 4.4E−02 ^(†)BP,Biological process; CC, cellular component; MF, molecular function^(††)DE, Differentially expressed genes ^(†††)FDR, False Discovery Rate

Consistent with our qRT-PCR findings (FIG. 24), analysis ofN-assimilation genes revealed a few key down-regulated genes that couldaccount for the low N-levels in the mutant, including nitrite reductase,two glutamine synthetases (GS1 and GS2), an ammonium transporter (AMT1)and a key enzyme involved in molybdenum cofactor biosynthesis(MoeA/CNX1), a cofactor that is essential for nitrate reductase activity(Table 29).

TABLE 32 Average Transcript Levels and Fold Changes of DifferentiallyExpressed Genes Involved in N-Assimilation ZnCys WT RNAi-7 FC^(††) GeneAlias N. gaditana id Description (FPKM) ^(†) (FPKM) ^(†) (log₂)FDR^(†††) Amt3 Naga_102173g1 Ammonium transporter 2.3 14.7 2.5 3.8E−06AmtB-like protein Amt2 Naga_100099g15 Ammonium transporter 635.9 841.40.4 5.5E−02 NAR2 Naga_100100g7 Formate nitrite transporter 40.3 42.7 0.18.3E−01 UreT Naga_100311g2 Urea active transporter- 6.4 6.5 −0.1 7.9E−01like protein NAR1 Naga_100046g36 Nitrite transporter 137.1 128.2 −0.15.2E−01 GOGAT2 Naga_100005g23 Glutamate synthase 54.1 48.9 −0.2 5.0E−01(plastid) GOGAT1 Naga_101084g2 Glutamate synthase 8.7 7.2 −0.3 7.3E−01NR Naga_100699g1 Nitrate reductase 336.1 283.2 −0.3 2.4E−01 NRT2NG_SCF17:5277-7851 Nitrate high affinity 1650.0 1368.4 −0.3 1.0E−02transporter GS1 Naga_100056g25 Glutamine synthetase 2084.4 1529.3 −0.53.4E−03 GDH1 Naga_100063g22 Glutamate dehydrogenase 317.5 205.4 −0.79.7E−06 GS2 Naga_100003g119 Glutamine synthetase 6.5 3.9 −0.7 4.3E−02NiR Naga_100852g1 Nitrite reductase 783.2 499.2 −0.7 2.3E−04 MoeA/CNX1Naga_101167g3 Molybdenum cofactor 207.0 83.0 −1.4 6.2E−14 biosynthesisprotein Amt1 Naga_100551g3 Ammonium transporter 126.9 16.7 −2.9 7.9E−36AmtB-like protein ^(†) FPKM, Fragments per kilobase of transcript permillion mapped reads ^(††)FC, Fold change of genes in ZnCys-RNAi-7relative to WT ^(†††)FDR, False Discovery Rate

The GO category analysis did not find a statistical enrichment for genesinvolved in lipid biosynthesis. However, when the list was manuallycurated, 26 genes related to glycerolipid biosynthesis were identifiedas upregulated using the same filtering criterium as above (Table 30).These genes included six fatty acid desaturases, elongases, lipases andacyltransferases of unknown substrate specificity, and the lipid dropletsurface protein (LDSP) which is believed to be the main structuralcomponent of the lipid droplet (Vieler et al. (2012) Plant Physiol.158:1562-1569).

TABLE 33 Average Transcript Levels and Fold Changes of DifferentiallyExpressed Genes Involved in Glycerolipid Biosynthesis ZnCys- WT RNAi-7FC^(††) N. gaditana id Description (FPKM) ^(†) (FPKM) ^(†) (log₂)FDR^(†††) Naga_100092g4 Omega-6 fatty acid desaturase delta-12 1.0 13.84.0 1.0E−11 Naga_100004g102 Elongation of fatty acids protein 19.6 120.02.6 2.9E−14 (EC 2.3.1.199) Naga_100086g4 Lipid droplet surface protein280.3 1608.6 2.5 7.4E−34 Naga_100040g9 Acyl transferase/acyl 0.7 2.0 2.27.9E−04 hydrolase/lysophospholipase Naga_100042g43 Nadp-dependentglyceraldehyde-3- 14.2 63.0 2.1 5.2E−08 phosphate dehydrogenaseNaga_100042g12 Delta 5 fatty acid desaturase 11.3 46.8 2.0 5.0E−11Naga_100035g27 CDP-diacylglycerol pyrophosphatase 1.0 4.3 2.0 3.2E−06Naga_100162g4 Elongation of fatty acids protein 7.3 28.5 1.9 5.9E−07 (EC2.3.1.199) Naga_100257g1 Glyceraldehyde-3-phosphate 20.0 74.9 1.82.2E−14 dehydrogenase (EC 1.2.1.12) Naga_100937g1 Acyltransferase 3(Fragment) 1.6 6.2 1.8 1.9E−04 Naga_100273g7 Delta 5 fatty aciddesaturase 12.2 42.2 1.8 2.4E−08 Naga_100001g58Glyceraldehyde-3-phosphate 25.8 87.8 1.7 4.8E−17 dehydrogenase (EC1.2.1.12) Naga_100426g5 Lipase, class 3 1.0 4.6 1.7 7.5E−05Naga_100012g35 Lipase domain-containing protein 0.3 1.6 1.6 2.8E−03Naga_100226g14 Acyltransferase 3 2.3 6.6 1.6 6.5E−07 Naga_100241g4Lipase 0.7 2.6 1.4 2.0E−03 Naga_100075g9 Delta (5) fatty acid desaturaseB 6.0 16.1 1.4 9.0E−05 Naga_100115g11 Stearoyl-CoA 9-desaturase 23.863.1 1.4 4.0E−14 Naga_102092g1 Acyl-CoA Synthase 5.3 13.1 1.3 8.5E−04Naga_100063g13 Delta 3 fatty acid desaturase 25.6 59.7 1.2 6.0E−09Naga_100530g1 Lipase-like protein 1.7 3.9 1.1 2.1E−02 Naga_100028g54Acetyl-coenzyme A synthetase 16.9 36.8 1.1 1.3E−10 (EC 6.2.1.1)Naga_101607g1 Triglyceride lipase-cholesterol esterase 53.7 115.3 1.11.9E−06 Naga_100247g4 Patatin-like phospholipase domain- 114.3 54.5 −1.12.0E−09 containing protein 2 Naga_100529g6 Lipase, class 3 (Fragment)291.2 134.6 −1.1 2.1E−13 Naga_100771g2 Acyltransferase 3 14.1 3.6 −2.05.4E−15 ^(†) FPKM, Fragments per kilobase of transcript per millionmapped reads ^(††)FC, Fold change of genes in ZnCys-RNAi-7 relative toWT ^(†††)FDR, False Discovery Rate (transcript levels are shown forgenes with FDR < 0.05)

Consistent with our Western blot data for ACCase and FAS (FIG. 25),transcripts encoding these enzymes were not found to be differentiallyexpressed in the mutant with respect to wild type, nor was differentialregulation of genes encoding diacylglycerol acyltransferases (DGATs) orother enzymatic steps leading to TAG biosynthesis observed.

What is claimed is:
 1. A classically-derived or genetically engineeredmutant algal or heterokont microorganism that produces at least 50% morefatty acid methyl ester-derivatizable lipids (FAME lipids) than acontrol microorganism and at least 70% of the amount of biomass producedby the control microorganism when the mutant microorganism and controlmicroorganism are cultured under identical conditions under which thecontrol microorganism is producing biomass, wherein the mutantmicroorganism has attenuated expression of a gene encoding a polypeptidecomprising an amino acid sequence having at least 80% identity to anamino acid sequence selected from the group consisting of SEQ ID NO:21,SEQ ID NO:22, SEQ ID NO:23, or SEQ ID NO:24.
 2. A mutant algal orheterokont microorganism according to claim 1, wherein the mutantmicroorganism and control microorganism are cultured under identicalconditions which are nitrogen replete with respect to the controlmicroorganism.
 3. A mutant algal or heterokont microorganism accordingto claim 1, wherein the control microorganism is a wild typemicroorganism.
 4. A mutant algal or heterokont microorganism accordingto claim 1, wherein the mutant microorganism produces at least 50% moreFAME lipids than a control microorganism while accumulating at least 70%the amount of biomass accumulated by the control microorganism over aculture period of at least five days.
 5. A mutant algal or heterokontmicroorganism according to claim 4, wherein the mutant microorganismproduces at least 50% more FAME lipids than a control microorganismwhile accumulating at least 70% the amount of biomass accumulated by thecontrol microorganism over a culture period of at least ten days.
 6. Amutant algal or heterokont microorganism according to claim 4, whereinthe mutant microorganism accumulates at least 80% the amount of biomassaccumulated by the control microorganism.
 7. A mutant algal orheterokont microorganism according to claim 6, wherein the mutantmicroorganism accumulates at least 90% the amount of biomass accumulatedby the control microorganism.
 8. A mutant algal or heterokontmicroorganism according to claim 7, wherein the mutant microorganismaccumulates at least 95% the amount of biomass accumulated by thecontrol microorganism.
 9. A mutant algal or heterokont microorganismaccording to claim 4, wherein the mutant microorganism produces at least75% more FAME lipids than the wild type microorganism.
 10. A mutantalgal or heterokont microorganism according to claim 9, wherein themutant microorganism produces at least 100% more FAME lipids than thecontrol microorganism.
 11. A mutant algal or heterokont microorganismaccording to claim 1, wherein the mutant microorganism exhibits aFAME/TOC ratio at least 30% higher than the FAME/TOC ratio of thecontrol microorganism.
 12. A mutant heterokont microorganism accordingto claim 1, wherein the heterokont microorganism is aLabyrinthulomycetes selected from the group consisting of the genera:Labryinthula, Labryinthuloides, Thraustochytrium, Schizochytrium,Aplanochytrium, Aurantiochytrium, Oblongichytrium, Japonochytrium,Diplophrys, or Ulkenia.
 13. A mutant heterokont microorganism accordingto claim 1, wherein the heterokont microorganism is aLabyrinthulomycetes species selected from a group consisting of thegenera Thraustochytrium, Schizochytrium, Aurantiochytrium,Oblongichytrium, and Japonochytrium.
 14. A mutant algal microorganismaccording to claim 1, wherein the algal microorganism is aEustigmatophyte.
 15. A mutant algal microorganism according to claim 14,wherein the Eustigmatophyte is of the genus Nannochloropsis.
 16. Amethod of producing lipid, comprising culturing the microorganism ofclaim 1 and isolating lipid from the microorganism, the culture medium,or both.
 17. A method of producing lipid, comprising culturing amicroorganism according to claim 1 under conditions in which the FAME toTOC ratio of the microorganism is maintained between 0.3 and 0.9, andisolating lipid from the microorganism, the culture medium, or both. 18.A method according to claim 16, wherein the FAME to TOC ratio ismaintained between about 0.4 and about 0.8.
 19. A method of producinglipid, comprising culturing a classical mutagenesis derived orgenetically engineered mutant algal or heterokont microorganism thatproduces at least 30% more fatty acid methyl ester-derivatizable lipids(FAME lipids) than a control algal or heterokont microorganism and atleast 45% of the amount of biomass produced by the control microorganismwhen the mutant microorganism and control microorganism are culturedunder identical conditions under which the control microorganism isproducing biomass, wherein the mutant microorganism has attenuatedexpression of a gene encoding a polypeptide comprising an amino acidsequence having at least 80% identity to an amino acid sequence selectedfrom the group consisting of: SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23,or SEQ ID NO:24.
 20. The method of claim 18 wherein the algalmicroorganism is a Eustigmatophyte.